2024-08-05T21:00:36,650 Created temporary directory: /tmp/pip-build-tracker-5fdenlcc 2024-08-05T21:00:36,652 Initialized build tracking at /tmp/pip-build-tracker-5fdenlcc 2024-08-05T21:00:36,652 Created build tracker: /tmp/pip-build-tracker-5fdenlcc 2024-08-05T21:00:36,652 Entered build tracker: /tmp/pip-build-tracker-5fdenlcc 2024-08-05T21:00:36,653 Created temporary directory: /tmp/pip-wheel-io3yiw1u 2024-08-05T21:00:36,657 Created temporary directory: /tmp/pip-ephem-wheel-cache-1grmpgl2 2024-08-05T21:00:36,687 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-08-05T21:00:36,690 2 location(s) to search for versions of uncalled4: 2024-08-05T21:00:36,690 * https://pypi.org/simple/uncalled4/ 2024-08-05T21:00:36,690 * https://www.piwheels.org/simple/uncalled4/ 2024-08-05T21:00:36,691 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2024-08-05T21:00:36,691 Getting page https://pypi.org/simple/uncalled4/ 2024-08-05T21:00:36,693 Found index url https://pypi.org/simple/ 2024-08-05T21:00:36,789 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2024-08-05T21:00:36,791 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 2024-08-05T21:00:36,792 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 2024-08-05T21:00:36,793 Found link https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz (from https://pypi.org/simple/uncalled4/) (requires-python:>=3.8), version: 4.0.1 2024-08-05T21:00:36,794 Found link https://files.pythonhosted.org/packages/3a/8a/a2753a224172a362f52c7cacaa69b993952bcf5cd2b816ce52ddcab6f156/uncalled4-4.1.0.tar.gz (from https://pypi.org/simple/uncalled4/) (requires-python:>=3.8), version: 4.1.0 2024-08-05T21:00:36,795 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2024-08-05T21:00:36,796 Getting page https://www.piwheels.org/simple/uncalled4/ 2024-08-05T21:00:36,797 Found index url https://www.piwheels.org/simple/ 2024-08-05T21:00:36,835 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2024-08-05T21:00:36,836 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2024-08-05T21:00:36,837 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2024-08-05T21:00:36,856 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2024-08-05T21:00:36,874 Collecting uncalled4==4.1.0 2024-08-05T21:00:36,877 Created temporary directory: /tmp/pip-unpack-bjejl6ot 2024-08-05T21:00:36,978 Downloading uncalled4-4.1.0.tar.gz (25.8 MB) 2024-08-05T21:00:43,503 Added uncalled4==4.1.0 from https://files.pythonhosted.org/packages/3a/8a/a2753a224172a362f52c7cacaa69b993952bcf5cd2b816ce52ddcab6f156/uncalled4-4.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-5fdenlcc' 2024-08-05T21:00:43,505 Running setup.py (path:/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/setup.py) egg_info for package uncalled4 2024-08-05T21:00:43,506 Created temporary directory: /tmp/pip-pip-egg-info-7pwy2ijh 2024-08-05T21:00:43,506 Preparing metadata (setup.py): started 2024-08-05T21:00:43,508 Running command python setup.py egg_info 2024-08-05T21:00:44,458 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:85: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-08-05T21:00:44,458 !! 2024-08-05T21:00:44,459 ******************************************************************************** 2024-08-05T21:00:44,460 Requirements should be satisfied by a PEP 517 installer. 2024-08-05T21:00:44,461 If you are using pip, you can try `pip install --use-pep517`. 2024-08-05T21:00:44,461 ******************************************************************************** 2024-08-05T21:00:44,463 !! 2024-08-05T21:00:44,463 dist.fetch_build_eggs(dist.setup_requires) 2024-08-05T21:00:46,996 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'build_backend' 2024-08-05T21:00:46,997 warnings.warn(msg) 2024-08-05T21:00:47,091 running egg_info 2024-08-05T21:00:47,093 creating /tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info 2024-08-05T21:00:47,122 writing /tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info/PKG-INFO 2024-08-05T21:00:47,125 writing dependency_links to /tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info/dependency_links.txt 2024-08-05T21:00:47,127 writing entry points to /tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info/entry_points.txt 2024-08-05T21:00:47,128 writing requirements to /tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info/requires.txt 2024-08-05T21:00:47,129 writing top-level names to /tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info/top_level.txt 2024-08-05T21:00:47,131 writing manifest file '/tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info/SOURCES.txt' 2024-08-05T21:00:47,258 reading manifest file '/tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info/SOURCES.txt' 2024-08-05T21:00:47,259 reading manifest template 'MANIFEST.in' 2024-08-05T21:00:47,310 adding license file 'LICENSE' 2024-08-05T21:00:47,316 writing manifest file '/tmp/pip-pip-egg-info-7pwy2ijh/uncalled4.egg-info/SOURCES.txt' 2024-08-05T21:00:47,435 Preparing metadata (setup.py): finished with status 'done' 2024-08-05T21:00:47,439 Source in /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f has version 4.1.0, which satisfies requirement uncalled4==4.1.0 from https://files.pythonhosted.org/packages/3a/8a/a2753a224172a362f52c7cacaa69b993952bcf5cd2b816ce52ddcab6f156/uncalled4-4.1.0.tar.gz 2024-08-05T21:00:47,440 Removed uncalled4==4.1.0 from https://files.pythonhosted.org/packages/3a/8a/a2753a224172a362f52c7cacaa69b993952bcf5cd2b816ce52ddcab6f156/uncalled4-4.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-5fdenlcc' 2024-08-05T21:00:47,447 Created temporary directory: /tmp/pip-unpack-vanfnunn 2024-08-05T21:00:47,448 Created temporary directory: /tmp/pip-unpack-unajqga6 2024-08-05T21:00:47,448 Building wheels for collected packages: uncalled4 2024-08-05T21:00:47,452 Created temporary directory: /tmp/pip-wheel-lk3p5g5d 2024-08-05T21:00:47,453 Building wheel for uncalled4 (setup.py): started 2024-08-05T21:00:47,454 Destination directory: /tmp/pip-wheel-lk3p5g5d 2024-08-05T21:00:47,455 Running command python setup.py bdist_wheel 2024-08-05T21:00:48,366 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:85: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-08-05T21:00:48,366 !! 2024-08-05T21:00:48,367 ******************************************************************************** 2024-08-05T21:00:48,367 Requirements should be satisfied by a PEP 517 installer. 2024-08-05T21:00:48,368 If you are using pip, you can try `pip install --use-pep517`. 2024-08-05T21:00:48,369 ******************************************************************************** 2024-08-05T21:00:48,370 !! 2024-08-05T21:00:48,370 dist.fetch_build_eggs(dist.setup_requires) 2024-08-05T21:00:48,609 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'build_backend' 2024-08-05T21:00:48,610 warnings.warn(msg) 2024-08-05T21:00:48,740 running bdist_wheel 2024-08-05T21:00:48,880 running build 2024-08-05T21:00:48,881 running build_py 2024-08-05T21:00:48,912 creating build 2024-08-05T21:00:48,913 creating build/lib.linux-armv7l-cpython-311 2024-08-05T21:00:48,913 creating build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,914 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,918 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,920 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,922 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,924 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,926 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,928 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,930 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,931 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,933 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,936 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,938 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,940 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,942 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-08-05T21:00:48,944 creating build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-08-05T21:00:48,945 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-08-05T21:00:48,947 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-08-05T21:00:48,948 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-08-05T21:00:48,950 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-08-05T21:00:48,952 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-08-05T21:00:48,953 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-08-05T21:00:48,955 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-08-05T21:00:48,957 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-08-05T21:00:48,959 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-08-05T21:00:48,961 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-08-05T21:00:48,963 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-08-05T21:00:48,966 creating build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-08-05T21:00:48,967 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-08-05T21:00:48,969 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-08-05T21:00:48,971 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-08-05T21:00:48,973 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-08-05T21:00:48,975 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-08-05T21:00:48,977 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-08-05T21:00:48,980 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-08-05T21:00:48,982 running egg_info 2024-08-05T21:00:49,010 writing src/uncalled4.egg-info/PKG-INFO 2024-08-05T21:00:49,014 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2024-08-05T21:00:49,015 writing entry points to src/uncalled4.egg-info/entry_points.txt 2024-08-05T21:00:49,017 writing requirements to src/uncalled4.egg-info/requires.txt 2024-08-05T21:00:49,018 writing top-level names to src/uncalled4.egg-info/top_level.txt 2024-08-05T21:00:49,053 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-08-05T21:00:49,057 reading manifest template 'MANIFEST.in' 2024-08-05T21:00:49,105 adding license file 'LICENSE' 2024-08-05T21:00:49,112 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-08-05T21:00:49,115 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2024-08-05T21:00:49,116 !! 2024-08-05T21:00:49,117 ******************************************************************************** 2024-08-05T21:00:49,117 ############################ 2024-08-05T21:00:49,117 # Package would be ignored # 2024-08-05T21:00:49,118 ############################ 2024-08-05T21:00:49,119 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2024-08-05T21:00:49,119 but it is absent from setuptools' `packages` configuration. 2024-08-05T21:00:49,120 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T21:00:49,121 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2024-08-05T21:00:49,121 to the `packages` configuration field. 2024-08-05T21:00:49,122 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T21:00:49,122 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T21:00:49,123 instead of `find_packages(...)`/`find:`). 2024-08-05T21:00:49,124 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T21:00:49,125 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T21:00:49,126 If you don't want 'uncalled4.__pycache__' to be distributed and are 2024-08-05T21:00:49,127 already explicitly excluding 'uncalled4.__pycache__' via 2024-08-05T21:00:49,127 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T21:00:49,128 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T21:00:49,129 combination with a more fine grained `package-data` configuration. 2024-08-05T21:00:49,130 You can read more about "package data files" on setuptools documentation page: 2024-08-05T21:00:49,131 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T21:00:49,133 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T21:00:49,133 even if it does not contain any `.py` files. 2024-08-05T21:00:49,134 On the other hand, currently there is no concept of package data 2024-08-05T21:00:49,134 directory, all directories are treated like packages. 2024-08-05T21:00:49,135 ******************************************************************************** 2024-08-05T21:00:49,136 !! 2024-08-05T21:00:49,137 check.warn(importable) 2024-08-05T21:00:49,137 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2024-08-05T21:00:49,138 !! 2024-08-05T21:00:49,139 ******************************************************************************** 2024-08-05T21:00:49,139 ############################ 2024-08-05T21:00:49,140 # Package would be ignored # 2024-08-05T21:00:49,141 ############################ 2024-08-05T21:00:49,141 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2024-08-05T21:00:49,142 but it is absent from setuptools' `packages` configuration. 2024-08-05T21:00:49,143 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T21:00:49,143 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2024-08-05T21:00:49,144 to the `packages` configuration field. 2024-08-05T21:00:49,145 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T21:00:49,146 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T21:00:49,146 instead of `find_packages(...)`/`find:`). 2024-08-05T21:00:49,147 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T21:00:49,148 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T21:00:49,149 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2024-08-05T21:00:49,150 already explicitly excluding 'uncalled4.io.__pycache__' via 2024-08-05T21:00:49,150 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T21:00:49,151 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T21:00:49,151 combination with a more fine grained `package-data` configuration. 2024-08-05T21:00:49,152 You can read more about "package data files" on setuptools documentation page: 2024-08-05T21:00:49,153 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T21:00:49,155 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T21:00:49,155 even if it does not contain any `.py` files. 2024-08-05T21:00:49,156 On the other hand, currently there is no concept of package data 2024-08-05T21:00:49,156 directory, all directories are treated like packages. 2024-08-05T21:00:49,157 ******************************************************************************** 2024-08-05T21:00:49,158 !! 2024-08-05T21:00:49,158 check.warn(importable) 2024-08-05T21:00:49,159 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2024-08-05T21:00:49,159 !! 2024-08-05T21:00:49,160 ******************************************************************************** 2024-08-05T21:00:49,161 ############################ 2024-08-05T21:00:49,161 # Package would be ignored # 2024-08-05T21:00:49,162 ############################ 2024-08-05T21:00:49,163 Python recognizes 'uncalled4.models' as an importable package[^1], 2024-08-05T21:00:49,163 but it is absent from setuptools' `packages` configuration. 2024-08-05T21:00:49,165 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T21:00:49,165 package, please make sure that 'uncalled4.models' is explicitly added 2024-08-05T21:00:49,166 to the `packages` configuration field. 2024-08-05T21:00:49,167 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T21:00:49,168 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T21:00:49,168 instead of `find_packages(...)`/`find:`). 2024-08-05T21:00:49,169 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T21:00:49,170 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T21:00:49,171 If you don't want 'uncalled4.models' to be distributed and are 2024-08-05T21:00:49,172 already explicitly excluding 'uncalled4.models' via 2024-08-05T21:00:49,172 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T21:00:49,174 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T21:00:49,174 combination with a more fine grained `package-data` configuration. 2024-08-05T21:00:49,176 You can read more about "package data files" on setuptools documentation page: 2024-08-05T21:00:49,177 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T21:00:49,178 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T21:00:49,179 even if it does not contain any `.py` files. 2024-08-05T21:00:49,179 On the other hand, currently there is no concept of package data 2024-08-05T21:00:49,179 directory, all directories are treated like packages. 2024-08-05T21:00:49,180 ******************************************************************************** 2024-08-05T21:00:49,181 !! 2024-08-05T21:00:49,182 check.warn(importable) 2024-08-05T21:00:49,182 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2024-08-05T21:00:49,183 !! 2024-08-05T21:00:49,188 ******************************************************************************** 2024-08-05T21:00:49,189 ############################ 2024-08-05T21:00:49,189 # Package would be ignored # 2024-08-05T21:00:49,190 ############################ 2024-08-05T21:00:49,190 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2024-08-05T21:00:49,191 but it is absent from setuptools' `packages` configuration. 2024-08-05T21:00:49,192 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T21:00:49,192 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2024-08-05T21:00:49,193 to the `packages` configuration field. 2024-08-05T21:00:49,193 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T21:00:49,194 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T21:00:49,194 instead of `find_packages(...)`/`find:`). 2024-08-05T21:00:49,195 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T21:00:49,197 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T21:00:49,198 If you don't want 'uncalled4.models.tombo' to be distributed and are 2024-08-05T21:00:49,198 already explicitly excluding 'uncalled4.models.tombo' via 2024-08-05T21:00:49,199 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T21:00:49,200 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T21:00:49,200 combination with a more fine grained `package-data` configuration. 2024-08-05T21:00:49,202 You can read more about "package data files" on setuptools documentation page: 2024-08-05T21:00:49,203 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T21:00:49,205 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T21:00:49,206 even if it does not contain any `.py` files. 2024-08-05T21:00:49,206 On the other hand, currently there is no concept of package data 2024-08-05T21:00:49,207 directory, all directories are treated like packages. 2024-08-05T21:00:49,207 ******************************************************************************** 2024-08-05T21:00:49,209 !! 2024-08-05T21:00:49,209 check.warn(importable) 2024-08-05T21:00:49,210 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2024-08-05T21:00:49,210 !! 2024-08-05T21:00:49,211 ******************************************************************************** 2024-08-05T21:00:49,212 ############################ 2024-08-05T21:00:49,213 # Package would be ignored # 2024-08-05T21:00:49,214 ############################ 2024-08-05T21:00:49,215 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2024-08-05T21:00:49,218 but it is absent from setuptools' `packages` configuration. 2024-08-05T21:00:49,244 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T21:00:49,264 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2024-08-05T21:00:49,274 to the `packages` configuration field. 2024-08-05T21:00:49,277 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T21:00:49,277 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T21:00:49,277 instead of `find_packages(...)`/`find:`). 2024-08-05T21:00:49,278 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T21:00:49,279 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T21:00:49,280 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2024-08-05T21:00:49,280 already explicitly excluding 'uncalled4.stats.__pycache__' via 2024-08-05T21:00:49,281 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T21:00:49,281 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T21:00:49,282 combination with a more fine grained `package-data` configuration. 2024-08-05T21:00:49,283 You can read more about "package data files" on setuptools documentation page: 2024-08-05T21:00:49,283 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T21:00:49,285 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T21:00:49,285 even if it does not contain any `.py` files. 2024-08-05T21:00:49,286 On the other hand, currently there is no concept of package data 2024-08-05T21:00:49,286 directory, all directories are treated like packages. 2024-08-05T21:00:49,287 ******************************************************************************** 2024-08-05T21:00:49,288 !! 2024-08-05T21:00:49,289 check.warn(importable) 2024-08-05T21:00:49,289 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2024-08-05T21:00:49,290 !! 2024-08-05T21:00:49,291 ******************************************************************************** 2024-08-05T21:00:49,291 ############################ 2024-08-05T21:00:49,292 # Package would be ignored # 2024-08-05T21:00:49,292 ############################ 2024-08-05T21:00:49,293 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2024-08-05T21:00:49,294 but it is absent from setuptools' `packages` configuration. 2024-08-05T21:00:49,295 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T21:00:49,296 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2024-08-05T21:00:49,296 to the `packages` configuration field. 2024-08-05T21:00:49,297 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T21:00:49,298 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T21:00:49,298 instead of `find_packages(...)`/`find:`). 2024-08-05T21:00:49,299 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T21:00:49,301 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T21:00:49,302 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2024-08-05T21:00:49,303 already explicitly excluding 'uncalled4.vis.__pycache__' via 2024-08-05T21:00:49,308 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T21:00:49,311 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T21:00:49,320 combination with a more fine grained `package-data` configuration. 2024-08-05T21:00:49,362 You can read more about "package data files" on setuptools documentation page: 2024-08-05T21:00:49,363 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T21:00:49,364 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T21:00:49,365 even if it does not contain any `.py` files. 2024-08-05T21:00:49,365 On the other hand, currently there is no concept of package data 2024-08-05T21:00:49,366 directory, all directories are treated like packages. 2024-08-05T21:00:49,366 ******************************************************************************** 2024-08-05T21:00:49,367 !! 2024-08-05T21:00:49,368 check.warn(importable) 2024-08-05T21:00:49,369 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2024-08-05T21:00:49,369 !! 2024-08-05T21:00:49,370 ******************************************************************************** 2024-08-05T21:00:49,371 ############################ 2024-08-05T21:00:49,371 # Package would be ignored # 2024-08-05T21:00:49,372 ############################ 2024-08-05T21:00:49,372 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2024-08-05T21:00:49,373 but it is absent from setuptools' `packages` configuration. 2024-08-05T21:00:49,374 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T21:00:49,374 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2024-08-05T21:00:49,375 to the `packages` configuration field. 2024-08-05T21:00:49,376 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T21:00:49,377 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T21:00:49,378 instead of `find_packages(...)`/`find:`). 2024-08-05T21:00:49,379 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T21:00:49,384 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T21:00:49,402 If you don't want 'uncalled4.vis.assets' to be distributed and are 2024-08-05T21:00:49,403 already explicitly excluding 'uncalled4.vis.assets' via 2024-08-05T21:00:49,404 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T21:00:49,404 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T21:00:49,405 combination with a more fine grained `package-data` configuration. 2024-08-05T21:00:49,406 You can read more about "package data files" on setuptools documentation page: 2024-08-05T21:00:49,407 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T21:00:49,408 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T21:00:49,409 even if it does not contain any `.py` files. 2024-08-05T21:00:49,410 On the other hand, currently there is no concept of package data 2024-08-05T21:00:49,410 directory, all directories are treated like packages. 2024-08-05T21:00:49,411 ******************************************************************************** 2024-08-05T21:00:49,412 !! 2024-08-05T21:00:49,413 check.warn(importable) 2024-08-05T21:00:49,413 creating build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,414 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,414 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,415 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,415 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,416 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,416 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,417 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,417 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,418 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,419 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,419 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,419 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,420 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,420 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,421 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,421 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,422 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,422 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,423 copying src/uncalled4/__pycache__/train.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-08-05T21:00:49,423 creating build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-08-05T21:00:49,424 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-08-05T21:00:49,424 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-08-05T21:00:49,425 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer_sh3.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-08-05T21:00:49,426 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-08-05T21:00:49,426 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-08-05T21:00:49,427 copying src/uncalled4/models/rna004_130bps_9mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-08-05T21:00:49,427 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-08-05T21:00:49,428 creating build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-08-05T21:00:49,428 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-08-05T21:00:49,429 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-08-05T21:00:49,429 creating build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,430 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,430 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,431 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,431 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,432 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,432 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,433 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,433 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,435 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,437 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,439 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,441 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,443 copying src/uncalled4/stats/__pycache__/readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,445 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,447 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-08-05T21:00:49,449 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,450 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,453 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,454 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,456 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,459 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,461 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,464 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,467 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,469 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,472 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,474 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,476 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,478 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,481 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,483 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-08-05T21:00:49,486 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-08-05T21:00:49,486 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-08-05T21:00:49,488 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-08-05T21:00:49,490 creating build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,491 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,493 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,496 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,498 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,501 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,503 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,505 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,507 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,510 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,513 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-08-05T21:00:49,517 running build_ext 2024-08-05T21:00:49,976 building '_uncalled4' extension 2024-08-05T21:00:49,997 creating build/temp.linux-armv7l-cpython-311 2024-08-05T21:00:49,998 creating build/temp.linux-armv7l-cpython-311/src 2024-08-05T21:00:49,999 creating build/temp.linux-armv7l-cpython-311/src/cpp 2024-08-05T21:00:50,000 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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 2024-08-05T21:00:55,990 In file included from src/cpp/dtw.hpp:7, 2024-08-05T21:00:55,990 from src/cpp/config.hpp:30, 2024-08-05T21:00:55,991 from src/cpp/config.cpp:1: 2024-08-05T21:00:55,992 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:00:55,993 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T21:00:55,993 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:00:55,994 192 | struct PyArray { 2024-08-05T21:00:55,995 | ^~~~~~~ 2024-08-05T21:00:56,226 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:00:56,227 src/cpp/read_buffer.hpp:99:38: required from here 2024-08-05T21:00:56,227 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:00:56,319 In file included from src/cpp/aln.hpp:11, 2024-08-05T21:00:56,319 from src/cpp/dtw.hpp:9: 2024-08-05T21:00:56,320 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-08-05T21:00:56,321 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:00:56,321 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-08-05T21:00:56,322 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-08-05T21:00:56,322 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:00:56,323 65 | while (i < events.size() && events[i].start < c.end) { 2024-08-05T21:00:56,348 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-08-05T21:00:56,349 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] 2024-08-05T21:00:56,350 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-08-05T21:00:56,350 | ~~^~~~~~~~~~ 2024-08-05T21:00:56,351 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-08-05T21:00:56,351 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] 2024-08-05T21:00:56,352 158 | normalize({0, events.size(), scale, shift}); 2024-08-05T21:00:56,353 | ~~~~~~~~~~~^~ 2024-08-05T21:00:56,418 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:00:56,419 src/cpp/event_detector.hpp:222:39: required from here 2024-08-05T21:00:56,419 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:00:56,420 192 | struct PyArray { 2024-08-05T21:00:56,421 | ^~~~~~~ 2024-08-05T21:00:56,539 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-08-05T21:00:56,540 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-08-05T21:00:56,541 188 | i64 ref; 2024-08-05T21:00:56,542 | ^~~ 2024-08-05T21:00:56,545 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-08-05T21:00:56,546 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-08-05T21:00:56,547 280 | int len,dist; 2024-08-05T21:00:56,547 | ^~~~ 2024-08-05T21:00:56,559 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:00:56,559 src/cpp/aln.hpp:385:23: required from here 2024-08-05T21:00:56,560 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:00:56,561 192 | struct PyArray { 2024-08-05T21:00:56,561 | ^~~~~~~ 2024-08-05T21:00:56,645 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:00:56,645 src/cpp/dtw.hpp:395:26: required from here 2024-08-05T21:00:56,646 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:01:14,194 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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 2024-08-05T21:01:20,347 In file included from src/cpp/dtw.hpp:7, 2024-08-05T21:01:20,348 from src/cpp/dtw.cpp:1: 2024-08-05T21:01:20,348 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:01:20,349 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T21:01:20,349 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:01:20,350 192 | struct PyArray { 2024-08-05T21:01:20,350 | ^~~~~~~ 2024-08-05T21:01:20,582 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:01:20,583 src/cpp/read_buffer.hpp:99:38: required from here 2024-08-05T21:01:20,583 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:01:20,674 In file included from src/cpp/aln.hpp:11, 2024-08-05T21:01:20,674 from src/cpp/dtw.hpp:9: 2024-08-05T21:01:20,675 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-08-05T21:01:20,676 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:01:20,676 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-08-05T21:01:20,677 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-08-05T21:01:20,677 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:01:20,678 65 | while (i < events.size() && events[i].start < c.end) { 2024-08-05T21:01:20,703 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-08-05T21:01:20,704 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] 2024-08-05T21:01:20,705 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-08-05T21:01:20,706 | ~~^~~~~~~~~~ 2024-08-05T21:01:20,706 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-08-05T21:01:20,707 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] 2024-08-05T21:01:20,708 158 | normalize({0, events.size(), scale, shift}); 2024-08-05T21:01:20,709 | ~~~~~~~~~~~^~ 2024-08-05T21:01:20,772 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:01:20,773 src/cpp/event_detector.hpp:222:39: required from here 2024-08-05T21:01:20,774 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:01:20,775 192 | struct PyArray { 2024-08-05T21:01:20,775 | ^~~~~~~ 2024-08-05T21:01:20,893 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-08-05T21:01:20,894 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-08-05T21:01:20,895 188 | i64 ref; 2024-08-05T21:01:20,895 | ^~~ 2024-08-05T21:01:20,899 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-08-05T21:01:20,899 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-08-05T21:01:20,900 280 | int len,dist; 2024-08-05T21:01:20,900 | ^~~~ 2024-08-05T21:01:20,912 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:01:20,913 src/cpp/aln.hpp:385:23: required from here 2024-08-05T21:01:20,913 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:01:20,914 192 | struct PyArray { 2024-08-05T21:01:20,914 | ^~~~~~~ 2024-08-05T21:01:20,998 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:01:20,999 src/cpp/dtw.hpp:395:26: required from here 2024-08-05T21:01:20,999 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:01:21,021 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2024-08-05T21:01:21,021 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2024-08-05T21:01:21,022 21 | size_t i = 0, j = 0, b = 0; 2024-08-05T21:01:21,022 | ^ 2024-08-05T21:01:21,026 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:01:21,027 src/cpp/dtw.cpp:64:30: required from here 2024-08-05T21:01:21,027 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:01:21,028 192 | struct PyArray { 2024-08-05T21:01:21,029 | ^~~~~~~ 2024-08-05T21:01:21,034 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2024-08-05T21:01:21,035 src/cpp/dtw.cpp:99:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2024-08-05T21:01:21,036 99 | auto fill = backfill_na ? samps : Interval(); 2024-08-05T21:01:21,037 | ^~~~ 2024-08-05T21:02:30,066 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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 2024-08-05T21:02:36,034 In file included from src/cpp/intervals.hpp:11, 2024-08-05T21:02:36,035 from src/cpp/event_detector.hpp:13, 2024-08-05T21:02:36,035 from src/cpp/event_detector.cpp:15: 2024-08-05T21:02:36,036 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:02:36,037 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T21:02:36,037 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:02:36,038 192 | struct PyArray { 2024-08-05T21:02:36,039 | ^~~~~~~ 2024-08-05T21:02:36,060 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:02:36,061 src/cpp/read_buffer.hpp:99:38: required from here 2024-08-05T21:02:36,062 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:02:36,175 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-08-05T21:02:36,176 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:02:36,177 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-08-05T21:02:36,177 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-08-05T21:02:36,178 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:02:36,178 65 | while (i < events.size() && events[i].start < c.end) { 2024-08-05T21:02:36,209 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-08-05T21:02:36,210 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] 2024-08-05T21:02:36,211 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-08-05T21:02:36,211 | ~~^~~~~~~~~~ 2024-08-05T21:02:36,212 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-08-05T21:02:36,212 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] 2024-08-05T21:02:36,213 158 | normalize({0, events.size(), scale, shift}); 2024-08-05T21:02:36,213 | ~~~~~~~~~~~^~ 2024-08-05T21:02:36,278 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:02:36,279 src/cpp/event_detector.hpp:222:39: required from here 2024-08-05T21:02:36,280 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:02:36,281 192 | struct PyArray { 2024-08-05T21:02:36,281 | ^~~~~~~ 2024-08-05T21:02:36,354 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:02:36,355 src/cpp/event_detector.cpp:250:30: required from here 2024-08-05T21:02:36,355 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:03:03,562 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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 2024-08-05T21:03:09,485 In file included from src/cpp/intervals.hpp:11, 2024-08-05T21:03:09,486 from src/cpp/intervals.cpp:2: 2024-08-05T21:03:09,487 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:03:09,487 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T21:03:09,488 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:03:09,489 192 | struct PyArray { 2024-08-05T21:03:09,489 | ^~~~~~~ 2024-08-05T21:03:11,737 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2024-08-05T21:03:11,738 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]’ 2024-08-05T21:03:11,739 src/cpp/intervals.cpp:7:31: required from here 2024-08-05T21:03:11,740 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] 2024-08-05T21:03:11,740 348 | while (gap >= MAX_LEN_I16) { 2024-08-05T21:03:11,741 | ~~~~^~~~~~~~~~~~~~ 2024-08-05T21:03:44,751 In file included from /usr/include/c++/12/vector:70, 2024-08-05T21:03:44,752 from src/cpp/intervals.hpp:6: 2024-08-05T21:03:44,753 /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 >]’: 2024-08-05T21:03:44,753 /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 2024-08-05T21:03:44,754 439 | vector<_Tp, _Alloc>:: 2024-08-05T21:03:44,754 | ^~~~~~~~~~~~~~~~~~~ 2024-08-05T21:03:44,848 In file included from /usr/include/c++/12/vector:64: 2024-08-05T21:03:44,849 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:44,849 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:44,850 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-08-05T21:03:44,851 inlined from ‘IntervalIndex IntervalIndex::mirror() const [with T = long long int]’ at src/cpp/intervals.hpp:160:23: 2024-08-05T21:03:44,851 /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 2024-08-05T21:03:44,852 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:44,853 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:03:44,946 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:44,947 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:44,947 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:235:23: 2024-08-05T21:03:44,948 /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 2024-08-05T21:03:44,949 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:44,949 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:03:44,950 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:44,951 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:44,952 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:237:27: 2024-08-05T21:03:44,953 /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 2024-08-05T21:03:44,953 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:44,954 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:03:44,955 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:44,956 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:44,956 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:242:19: 2024-08-05T21:03:44,957 /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 2024-08-05T21:03:44,957 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:44,958 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:03:45,185 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:45,185 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:45,186 inlined from ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:202:27: 2024-08-05T21:03:45,186 /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 2024-08-05T21:03:45,187 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:45,187 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:03:45,188 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:45,189 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:45,190 inlined from ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:212:19: 2024-08-05T21:03:45,190 /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 2024-08-05T21:03:45,191 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:45,192 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:03:46,221 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:46,221 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:46,222 inlined from ‘IntervalIndex IntervalIndex::intersect(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:176:31: 2024-08-05T21:03:46,223 /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 2024-08-05T21:03:46,223 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:46,224 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:03:59,513 /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 >]’: 2024-08-05T21:03:59,513 /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 2024-08-05T21:03:59,514 439 | vector<_Tp, _Alloc>:: 2024-08-05T21:03:59,514 | ^~~~~~~~~~~~~~~~~~~ 2024-08-05T21:03:59,592 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2024-08-05T21:03:59,593 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, 2024-08-05T21:03:59,593 inlined from ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector, std::allocator > >; Value = std::pair]’ at /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/stl.h:180:28: 2024-08-05T21:03:59,594 /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 2024-08-05T21:03:59,595 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-08-05T21:03:59,595 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-08-05T21:03:59,817 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:59,818 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:59,818 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-08-05T21:03:59,819 inlined from ‘void IntervalIndex::init_coords(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:134:19, 2024-08-05T21:03:59,820 inlined from ‘IntervalIndex::IntervalIndex(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:101:20, 2024-08-05T21:03:59,821 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12, 2024-08-05T21:03:59,821 inlined from ‘pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>’ at /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70, 2024-08-05T21:03:59,822 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1624:37, 2024-08-05T21:03:59,823 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1598:65, 2024-08-05T21:03:59,824 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:293:78, 2024-08-05T21:03:59,825 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:267:21: 2024-08-05T21:03:59,825 /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 2024-08-05T21:03:59,826 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:59,827 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:03:59,828 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-08-05T21:03:59,828 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-08-05T21:03:59,829 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-08-05T21:03:59,830 inlined from ‘void IntervalIndex::init_coords(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:134:19, 2024-08-05T21:03:59,830 inlined from ‘IntervalIndex::IntervalIndex(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:101:20, 2024-08-05T21:03:59,831 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12, 2024-08-05T21:03:59,832 inlined from ‘pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>’ at /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70, 2024-08-05T21:03:59,833 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1624:37, 2024-08-05T21:03:59,833 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1598:65, 2024-08-05T21:03:59,834 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:297:75, 2024-08-05T21:03:59,835 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-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:267:21: 2024-08-05T21:03:59,836 /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 2024-08-05T21:03:59,836 1287 | _M_realloc_insert(end(), __x); 2024-08-05T21:03:59,837 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T21:04:08,470 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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 2024-08-05T21:04:20,380 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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 2024-08-05T21:04:26,270 In file included from src/cpp/pore_model.hpp:36, 2024-08-05T21:04:26,271 from src/cpp/pore_model.cpp:1: 2024-08-05T21:04:26,272 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:04:26,272 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T21:04:26,273 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:04:26,274 192 | struct PyArray { 2024-08-05T21:04:26,275 | ^~~~~~~ 2024-08-05T21:05:02,801 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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 2024-08-05T21:05:08,759 In file included from src/cpp/read_buffer.hpp:30, 2024-08-05T21:05:08,760 from src/cpp/pybinder.cpp:5: 2024-08-05T21:05:08,761 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:05:08,762 src/cpp/read_buffer.hpp:99:38: required from here 2024-08-05T21:05:08,762 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:05:08,763 192 | struct PyArray { 2024-08-05T21:05:08,764 | ^~~~~~~ 2024-08-05T21:05:08,792 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:05:08,793 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T21:05:08,794 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:05:08,909 In file included from src/cpp/signal_processor.hpp:7, 2024-08-05T21:05:08,909 from src/cpp/pybinder.cpp:6: 2024-08-05T21:05:08,910 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-08-05T21:05:08,911 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:05:08,911 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-08-05T21:05:08,912 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-08-05T21:05:08,913 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:05:08,913 65 | while (i < events.size() && events[i].start < c.end) { 2024-08-05T21:05:08,943 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-08-05T21:05:08,944 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] 2024-08-05T21:05:08,944 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-08-05T21:05:08,945 | ~~^~~~~~~~~~ 2024-08-05T21:05:08,945 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-08-05T21:05:08,946 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] 2024-08-05T21:05:08,947 158 | normalize({0, events.size(), scale, shift}); 2024-08-05T21:05:08,947 | ~~~~~~~~~~~^~ 2024-08-05T21:05:09,013 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:05:09,014 src/cpp/event_detector.hpp:222:39: required from here 2024-08-05T21:05:09,014 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:05:09,015 192 | struct PyArray { 2024-08-05T21:05:09,016 | ^~~~~~~ 2024-08-05T21:05:09,317 In file included from src/cpp/dtw.hpp:9, 2024-08-05T21:05:09,318 from src/cpp/pybinder.cpp:8: 2024-08-05T21:05:09,319 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-08-05T21:05:09,319 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-08-05T21:05:09,320 188 | i64 ref; 2024-08-05T21:05:09,321 | ^~~ 2024-08-05T21:05:09,323 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-08-05T21:05:09,324 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-08-05T21:05:09,325 280 | int len,dist; 2024-08-05T21:05:09,325 | ^~~~ 2024-08-05T21:05:09,336 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:05:09,337 src/cpp/aln.hpp:385:23: required from here 2024-08-05T21:05:09,338 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:05:09,338 192 | struct PyArray { 2024-08-05T21:05:09,339 | ^~~~~~~ 2024-08-05T21:05:09,422 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:05:09,423 src/cpp/dtw.hpp:395:26: required from here 2024-08-05T21:05:09,423 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:05:09,467 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:05:09,468 src/cpp/eventalign.hpp:110:31: required from here 2024-08-05T21:05:09,469 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:05:13,257 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:05:13,258 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]’ 2024-08-05T21:05:13,258 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]’ 2024-08-05T21:05:13,259 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:13,260 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:05:13,289 In file included from src/cpp/pybinder.cpp:10: 2024-08-05T21:05:13,290 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]’: 2024-08-05T21:05:13,290 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]’ 2024-08-05T21:05:13,291 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:13,292 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:05:13,292 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-08-05T21:05:13,293 | ~~^~~~~~~~~~~ 2024-08-05T21:05:13,480 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T21:05:13,481 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]’ 2024-08-05T21:05:13,481 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]’ 2024-08-05T21:05:13,482 src/cpp/pybinder.cpp:67:22: required from here 2024-08-05T21:05:13,483 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T21:05:13,484 192 | struct PyArray { 2024-08-05T21:05:13,484 | ^~~~~~~ 2024-08-05T21:05:13,510 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]’: 2024-08-05T21:05:13,511 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]’ 2024-08-05T21:05:13,512 src/cpp/pybinder.cpp:67:22: required from here 2024-08-05T21:05:13,513 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T21:05:13,513 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-08-05T21:05:13,514 | ~~^~~~~~~~~~~ 2024-08-05T21:05:20,307 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-08-05T21:05:20,308 src/cpp/dtw.hpp:736:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:20,309 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]’ 2024-08-05T21:05:20,309 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:20,310 src/cpp/dtw.hpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-08-05T21:05:20,310 646 | if (q0 >= qry_size()) { 2024-08-05T21:05:20,311 | ~~~^~~~~~~~~~~~~ 2024-08-05T21:05:20,311 src/cpp/dtw.hpp:653:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-08-05T21:05:20,312 653 | if (r1 > ref_size()) { 2024-08-05T21:05:20,313 | ~~~^~~~~~~~~~~~ 2024-08-05T21:05:20,837 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-08-05T21:05:20,838 src/cpp/dtw.hpp:736:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:20,839 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]’ 2024-08-05T21:05:20,840 src/cpp/pybinder.cpp:67:22: required from here 2024-08-05T21:05:20,841 src/cpp/dtw.hpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-08-05T21:05:20,841 646 | if (q0 >= qry_size()) { 2024-08-05T21:05:20,842 | ~~~^~~~~~~~~~~~~ 2024-08-05T21:05:20,843 src/cpp/dtw.hpp:653:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-08-05T21:05:20,843 653 | if (r1 > ref_size()) { 2024-08-05T21:05:20,844 | ~~~^~~~~~~~~~~~ 2024-08-05T21:05:31,725 In file included from src/cpp/seq.hpp:32, 2024-08-05T21:05:31,725 from src/cpp/pybinder.cpp:7: 2024-08-05T21:05:31,726 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]’: 2024-08-05T21:05:31,727 src/cpp/pore_model.hpp:505:32: 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]’ 2024-08-05T21:05:31,728 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:31,728 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:31,729 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]’ 2024-08-05T21:05:31,730 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:31,730 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-08-05T21:05:31,731 516 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2024-08-05T21:05:31,732 | ~~~~~~~~~~^ 2024-08-05T21:05:31,732 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]’: 2024-08-05T21:05:31,733 src/cpp/pore_model.hpp:507:32: 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]’ 2024-08-05T21:05:31,733 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:31,734 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:31,735 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]’ 2024-08-05T21:05:31,735 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:31,736 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-08-05T21:05:34,531 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]’: 2024-08-05T21:05:34,532 src/cpp/pore_model.hpp:505:32: 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]’ 2024-08-05T21:05:34,533 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:34,534 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:34,535 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]’ 2024-08-05T21:05:34,535 src/cpp/pybinder.cpp:67:22: required from here 2024-08-05T21:05:34,536 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-08-05T21:05:34,537 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]’: 2024-08-05T21:05:34,538 src/cpp/pore_model.hpp:507:32: 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]’ 2024-08-05T21:05:34,538 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:34,539 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:34,540 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]’ 2024-08-05T21:05:34,540 src/cpp/pybinder.cpp:67:22: required from here 2024-08-05T21:05:34,541 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-08-05T21:05:41,922 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]’: 2024-08-05T21:05:41,922 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-08-05T21:05:41,923 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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]’ 2024-08-05T21:05:41,923 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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}]’ 2024-08-05T21:05:41,924 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:1707:21: 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 = {}]’ 2024-08-05T21:05:41,925 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:41,926 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]’ 2024-08-05T21:05:41,926 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:41,927 src/cpp/pore_model.hpp:355:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-08-05T21:05:41,928 355 | auto get_kmer = [&](size_t i) {return i;}; 2024-08-05T21:05:41,929 | ^~~~~~~~ 2024-08-05T21:05:42,621 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-08-05T21:05:42,622 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]’ 2024-08-05T21:05:42,622 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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]’ 2024-08-05T21:05:42,623 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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&}]’ 2024-08-05T21:05:42,623 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:1707:21: 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 = {}]’ 2024-08-05T21:05:42,624 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:42,625 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]’ 2024-08-05T21:05:42,626 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:42,626 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] 2024-08-05T21:05:42,627 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-08-05T21:05:42,628 | ~~^~~~~~~~~~~~ 2024-08-05T21:05:42,628 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-08-05T21:05:42,629 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]’ 2024-08-05T21:05:42,630 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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]’ 2024-08-05T21:05:42,631 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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&}]’ 2024-08-05T21:05:42,631 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:1707:21: 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 = {}]’ 2024-08-05T21:05:42,632 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:42,633 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]’ 2024-08-05T21:05:42,633 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:42,634 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] 2024-08-05T21:05:42,635 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-08-05T21:05:42,635 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-08-05T21:05:43,511 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]’: 2024-08-05T21:05:43,512 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2024-08-05T21:05:43,512 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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]’ 2024-08-05T21:05:43,513 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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}]’ 2024-08-05T21:05:43,514 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:1707:21: 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 = {}]’ 2024-08-05T21:05:43,515 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:43,515 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]’ 2024-08-05T21:05:43,516 src/cpp/pybinder.cpp:67:22: required from here 2024-08-05T21:05:43,517 src/cpp/pore_model.hpp:355:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-08-05T21:05:43,517 355 | auto get_kmer = [&](size_t i) {return i;}; 2024-08-05T21:05:43,518 | ^~~~~~~~ 2024-08-05T21:05:43,707 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-08-05T21:05:43,708 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]’ 2024-08-05T21:05:43,709 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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]’ 2024-08-05T21:05:43,710 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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&}]’ 2024-08-05T21:05:43,711 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:1707:21: 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 = {}]’ 2024-08-05T21:05:43,711 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:43,713 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]’ 2024-08-05T21:05:43,714 src/cpp/pybinder.cpp:67:22: required from here 2024-08-05T21:05:43,714 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] 2024-08-05T21:05:43,715 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-08-05T21:05:43,716 | ~~^~~~~~~~~~~~ 2024-08-05T21:05:43,717 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-08-05T21:05:43,719 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]’ 2024-08-05T21:05:43,721 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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]’ 2024-08-05T21:05:43,722 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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&}]’ 2024-08-05T21:05:43,724 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:1707:21: 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 = {}]’ 2024-08-05T21:05:43,725 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:43,727 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]’ 2024-08-05T21:05:43,730 src/cpp/pybinder.cpp:67:22: required from here 2024-08-05T21:05:43,731 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] 2024-08-05T21:05:43,734 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-08-05T21:05:43,735 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-08-05T21:05:44,907 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2024-08-05T21:05:44,908 src/cpp/pore_model.hpp:378:45: required from ‘void PoreModel::init_current(const Container&, const Container&, const Container&, const Container&, bool) [with Container = PyArray; KmerType = short unsigned int]’ 2024-08-05T21:05:44,909 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-08-05T21:05:44,909 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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]’ 2024-08-05T21:05:44,910 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-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}]’ 2024-08-05T21:05:44,911 /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/.eggs/pybind11-2.13.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:1707:21: 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 = {}]’ 2024-08-05T21:05:44,911 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T21:05:44,912 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]’ 2024-08-05T21:05:44,913 src/cpp/pybinder.cpp:66:22: required from here 2024-08-05T21:05:44,913 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2024-08-05T21:05:44,914 144 | auto sum = super::sum(); 2024-08-05T21:05:44,915 | ^~~ 2024-08-05T21:05:44,916 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2024-08-05T21:05:44,916 145 | auto len = super::size(); 2024-08-05T21:05:44,917 | ^~~ 2024-08-05T21:06:24,103 cc1plus: out of memory allocating 20566080 bytes after a total of 23818240 bytes 2024-08-05T21:06:24,228 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-08-05T21:06:24,377 ERROR: python setup.py bdist_wheel exited with 1 2024-08-05T21:06:24,390 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2024-08-05T21:06:24,390 exec(compile('"'"''"'"''"'"' 2024-08-05T21:06:24,390 # This is -- a caller that pip uses to run setup.py 2024-08-05T21:06:24,390 # 2024-08-05T21:06:24,390 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-08-05T21:06:24,390 # import from `distutils.core` to work with newer packaging standards. 2024-08-05T21:06:24,390 # - It provides a clear error message when setuptools is not installed. 2024-08-05T21:06:24,390 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-08-05T21:06:24,390 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-08-05T21:06:24,390 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-08-05T21:06:24,390 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-08-05T21:06:24,390 import os, sys, tokenize 2024-08-05T21:06:24,390 2024-08-05T21:06:24,390 try: 2024-08-05T21:06:24,390 import setuptools 2024-08-05T21:06:24,390 except ImportError as error: 2024-08-05T21:06:24,390 print( 2024-08-05T21:06:24,390 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-08-05T21:06:24,390 "the build environment.", 2024-08-05T21:06:24,390 file=sys.stderr, 2024-08-05T21:06:24,390 ) 2024-08-05T21:06:24,390 sys.exit(1) 2024-08-05T21:06:24,390 2024-08-05T21:06:24,390 __file__ = %r 2024-08-05T21:06:24,390 sys.argv[0] = __file__ 2024-08-05T21:06:24,390 2024-08-05T21:06:24,390 if os.path.exists(__file__): 2024-08-05T21:06:24,390 filename = __file__ 2024-08-05T21:06:24,390 with tokenize.open(__file__) as f: 2024-08-05T21:06:24,390 setup_py_code = f.read() 2024-08-05T21:06:24,390 else: 2024-08-05T21:06:24,390 filename = "" 2024-08-05T21:06:24,390 setup_py_code = "from setuptools import setup; setup()" 2024-08-05T21:06:24,390 2024-08-05T21:06:24,390 exec(compile(setup_py_code, filename, "exec")) 2024-08-05T21:06:24,390 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-lk3p5g5d[/] 2024-08-05T21:06:24,391 [bold magenta]cwd[/]: /tmp/pip-wheel-io3yiw1u/uncalled4_d092e325644e4747a23e7849936c5a4f/ 2024-08-05T21:06:24,392 Building wheel for uncalled4 (setup.py): finished with status 'error' 2024-08-05T21:06:24,393 ERROR: Failed building wheel for uncalled4 2024-08-05T21:06:24,394 Running setup.py clean for uncalled4 2024-08-05T21:06:24,395 Running command python setup.py clean 2024-08-05T21:06:25,395 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:85: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-08-05T21:06:25,396 !! 2024-08-05T21:06:25,397 ******************************************************************************** 2024-08-05T21:06:25,397 Requirements should be satisfied by a PEP 517 installer. 2024-08-05T21:06:25,398 If you are using pip, you can try `pip install --use-pep517`. 2024-08-05T21:06:25,399 ******************************************************************************** 2024-08-05T21:06:25,400 !! 2024-08-05T21:06:25,400 dist.fetch_build_eggs(dist.setup_requires) 2024-08-05T21:06:25,637 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'build_backend' 2024-08-05T21:06:25,638 warnings.warn(msg) 2024-08-05T21:06:25,802 running clean 2024-08-05T21:06:25,858 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2024-08-05T21:06:25,874 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2024-08-05T21:06:25,905 'build/bdist.linux-armv7l' does not exist -- can't clean it 2024-08-05T21:06:25,906 'build/scripts-3.11' does not exist -- can't clean it 2024-08-05T21:06:25,906 removing 'build' 2024-08-05T21:06:26,025 Failed to build uncalled4 2024-08-05T21:06:26,026 ERROR: Failed to build one or more wheels 2024-08-05T21:06:26,028 Exception information: 2024-08-05T21:06:26,028 Traceback (most recent call last): 2024-08-05T21:06:26,028 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 179, in exc_logging_wrapper 2024-08-05T21:06:26,028 status = run_func(*args) 2024-08-05T21:06:26,028 ^^^^^^^^^^^^^^^ 2024-08-05T21:06:26,028 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 67, in wrapper 2024-08-05T21:06:26,028 return func(self, options, args) 2024-08-05T21:06:26,028 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-08-05T21:06:26,028 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2024-08-05T21:06:26,028 raise CommandError("Failed to build one or more wheels") 2024-08-05T21:06:26,028 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-08-05T21:06:26,031 Removed build tracker: '/tmp/pip-build-tracker-5fdenlcc'