2024-08-05T22:01:35,850 Created temporary directory: /tmp/pip-build-tracker-g94lcvgj 2024-08-05T22:01:35,851 Initialized build tracking at /tmp/pip-build-tracker-g94lcvgj 2024-08-05T22:01:35,851 Created build tracker: /tmp/pip-build-tracker-g94lcvgj 2024-08-05T22:01:35,851 Entered build tracker: /tmp/pip-build-tracker-g94lcvgj 2024-08-05T22:01:35,852 Created temporary directory: /tmp/pip-wheel-firjgvdh 2024-08-05T22:01:35,857 Created temporary directory: /tmp/pip-ephem-wheel-cache-kns33y1n 2024-08-05T22:01:35,888 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-08-05T22:01:35,891 2 location(s) to search for versions of uncalled4: 2024-08-05T22:01:35,891 * https://pypi.org/simple/uncalled4/ 2024-08-05T22:01:35,891 * https://www.piwheels.org/simple/uncalled4/ 2024-08-05T22:01:35,891 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2024-08-05T22:01:35,892 Getting page https://pypi.org/simple/uncalled4/ 2024-08-05T22:01:35,893 Found index url https://pypi.org/simple/ 2024-08-05T22:01:35,996 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2024-08-05T22:01:35,998 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 2024-08-05T22:01:35,998 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 2024-08-05T22:01:35,999 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 2024-08-05T22:01:35,999 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 2024-08-05T22:01:36,000 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2024-08-05T22:01:36,000 Getting page https://www.piwheels.org/simple/uncalled4/ 2024-08-05T22:01:36,001 Found index url https://www.piwheels.org/simple/ 2024-08-05T22:01:36,034 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2024-08-05T22:01:36,035 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2024-08-05T22:01:36,035 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2024-08-05T22:01:36,053 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2024-08-05T22:01:36,070 Collecting uncalled4==4.1.0 2024-08-05T22:01:36,072 Created temporary directory: /tmp/pip-unpack-bxjlc9o_ 2024-08-05T22:01:36,091 Downloading uncalled4-4.1.0.tar.gz (25.8 MB) 2024-08-05T22:01:40,281 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-g94lcvgj' 2024-08-05T22:01:40,284 Running setup.py (path:/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/setup.py) egg_info for package uncalled4 2024-08-05T22:01:40,285 Created temporary directory: /tmp/pip-pip-egg-info-cht9uhsc 2024-08-05T22:01:40,285 Preparing metadata (setup.py): started 2024-08-05T22:01:40,286 Running command python setup.py egg_info 2024-08-05T22:01:41,278 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:85: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-08-05T22:01:41,278 !! 2024-08-05T22:01:41,278 ******************************************************************************** 2024-08-05T22:01:41,278 Requirements should be satisfied by a PEP 517 installer. 2024-08-05T22:01:41,279 If you are using pip, you can try `pip install --use-pep517`. 2024-08-05T22:01:41,279 ******************************************************************************** 2024-08-05T22:01:41,279 !! 2024-08-05T22:01:41,279 dist.fetch_build_eggs(dist.setup_requires) 2024-08-05T22:01:43,777 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'build_backend' 2024-08-05T22:01:43,778 warnings.warn(msg) 2024-08-05T22:01:43,874 running egg_info 2024-08-05T22:01:43,876 creating /tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info 2024-08-05T22:01:43,904 writing /tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info/PKG-INFO 2024-08-05T22:01:43,907 writing dependency_links to /tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info/dependency_links.txt 2024-08-05T22:01:43,908 writing entry points to /tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info/entry_points.txt 2024-08-05T22:01:43,910 writing requirements to /tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info/requires.txt 2024-08-05T22:01:43,911 writing top-level names to /tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info/top_level.txt 2024-08-05T22:01:43,913 writing manifest file '/tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info/SOURCES.txt' 2024-08-05T22:01:44,037 reading manifest file '/tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info/SOURCES.txt' 2024-08-05T22:01:44,039 reading manifest template 'MANIFEST.in' 2024-08-05T22:01:44,091 adding license file 'LICENSE' 2024-08-05T22:01:44,098 writing manifest file '/tmp/pip-pip-egg-info-cht9uhsc/uncalled4.egg-info/SOURCES.txt' 2024-08-05T22:01:44,198 Preparing metadata (setup.py): finished with status 'done' 2024-08-05T22:01:44,203 Source in /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575 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 2024-08-05T22:01:44,204 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-g94lcvgj' 2024-08-05T22:01:44,213 Created temporary directory: /tmp/pip-unpack-4z21q9id 2024-08-05T22:01:44,214 Created temporary directory: /tmp/pip-unpack-lruthjsy 2024-08-05T22:01:44,215 Building wheels for collected packages: uncalled4 2024-08-05T22:01:44,218 Created temporary directory: /tmp/pip-wheel-ygakpr6p 2024-08-05T22:01:44,219 Building wheel for uncalled4 (setup.py): started 2024-08-05T22:01:44,219 Destination directory: /tmp/pip-wheel-ygakpr6p 2024-08-05T22:01:44,220 Running command python setup.py bdist_wheel 2024-08-05T22:01:45,116 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:85: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-08-05T22:01:45,117 !! 2024-08-05T22:01:45,117 ******************************************************************************** 2024-08-05T22:01:45,117 Requirements should be satisfied by a PEP 517 installer. 2024-08-05T22:01:45,117 If you are using pip, you can try `pip install --use-pep517`. 2024-08-05T22:01:45,118 ******************************************************************************** 2024-08-05T22:01:45,118 !! 2024-08-05T22:01:45,118 dist.fetch_build_eggs(dist.setup_requires) 2024-08-05T22:01:45,340 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'build_backend' 2024-08-05T22:01:45,340 warnings.warn(msg) 2024-08-05T22:01:45,475 running bdist_wheel 2024-08-05T22:01:45,610 running build 2024-08-05T22:01:45,610 running build_py 2024-08-05T22:01:45,641 creating build 2024-08-05T22:01:45,641 creating build/lib.linux-armv7l-cpython-39 2024-08-05T22:01:45,642 creating build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,643 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,645 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,646 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,649 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,650 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,653 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,655 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,657 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,659 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,662 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,664 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,666 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,668 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,670 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-08-05T22:01:45,673 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-08-05T22:01:45,674 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-08-05T22:01:45,675 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-08-05T22:01:45,678 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-08-05T22:01:45,679 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-08-05T22:01:45,681 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-08-05T22:01:45,683 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-08-05T22:01:45,686 creating build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-08-05T22:01:45,687 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-08-05T22:01:45,689 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-08-05T22:01:45,691 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-08-05T22:01:45,693 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-08-05T22:01:45,695 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-08-05T22:01:45,697 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-08-05T22:01:45,699 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-08-05T22:01:45,701 creating build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-08-05T22:01:45,702 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-08-05T22:01:45,703 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-08-05T22:01:45,705 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-08-05T22:01:45,707 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-08-05T22:01:45,708 running egg_info 2024-08-05T22:01:45,735 writing src/uncalled4.egg-info/PKG-INFO 2024-08-05T22:01:45,738 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2024-08-05T22:01:45,740 writing entry points to src/uncalled4.egg-info/entry_points.txt 2024-08-05T22:01:45,742 writing requirements to src/uncalled4.egg-info/requires.txt 2024-08-05T22:01:45,743 writing top-level names to src/uncalled4.egg-info/top_level.txt 2024-08-05T22:01:45,779 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-08-05T22:01:45,784 reading manifest template 'MANIFEST.in' 2024-08-05T22:01:45,833 adding license file 'LICENSE' 2024-08-05T22:01:45,842 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-08-05T22:01:45,847 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2024-08-05T22:01:45,847 !! 2024-08-05T22:01:45,847 ******************************************************************************** 2024-08-05T22:01:45,847 ############################ 2024-08-05T22:01:45,847 # Package would be ignored # 2024-08-05T22:01:45,847 ############################ 2024-08-05T22:01:45,848 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2024-08-05T22:01:45,848 but it is absent from setuptools' `packages` configuration. 2024-08-05T22:01:45,848 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T22:01:45,848 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2024-08-05T22:01:45,848 to the `packages` configuration field. 2024-08-05T22:01:45,848 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T22:01:45,849 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T22:01:45,849 instead of `find_packages(...)`/`find:`). 2024-08-05T22:01:45,849 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T22:01:45,849 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T22:01:45,849 If you don't want 'uncalled4.__pycache__' to be distributed and are 2024-08-05T22:01:45,849 already explicitly excluding 'uncalled4.__pycache__' via 2024-08-05T22:01:45,850 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T22:01:45,850 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T22:01:45,850 combination with a more fine grained `package-data` configuration. 2024-08-05T22:01:45,850 You can read more about "package data files" on setuptools documentation page: 2024-08-05T22:01:45,850 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T22:01:45,851 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T22:01:45,851 even if it does not contain any `.py` files. 2024-08-05T22:01:45,851 On the other hand, currently there is no concept of package data 2024-08-05T22:01:45,851 directory, all directories are treated like packages. 2024-08-05T22:01:45,851 ******************************************************************************** 2024-08-05T22:01:45,851 !! 2024-08-05T22:01:45,851 check.warn(importable) 2024-08-05T22:01:45,852 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2024-08-05T22:01:45,852 !! 2024-08-05T22:01:45,852 ******************************************************************************** 2024-08-05T22:01:45,852 ############################ 2024-08-05T22:01:45,852 # Package would be ignored # 2024-08-05T22:01:45,852 ############################ 2024-08-05T22:01:45,852 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2024-08-05T22:01:45,853 but it is absent from setuptools' `packages` configuration. 2024-08-05T22:01:45,853 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T22:01:45,853 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2024-08-05T22:01:45,853 to the `packages` configuration field. 2024-08-05T22:01:45,853 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T22:01:45,853 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T22:01:45,854 instead of `find_packages(...)`/`find:`). 2024-08-05T22:01:45,854 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T22:01:45,854 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T22:01:45,854 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2024-08-05T22:01:45,854 already explicitly excluding 'uncalled4.io.__pycache__' via 2024-08-05T22:01:45,854 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T22:01:45,855 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T22:01:45,855 combination with a more fine grained `package-data` configuration. 2024-08-05T22:01:45,855 You can read more about "package data files" on setuptools documentation page: 2024-08-05T22:01:45,855 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T22:01:45,856 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T22:01:45,856 even if it does not contain any `.py` files. 2024-08-05T22:01:45,856 On the other hand, currently there is no concept of package data 2024-08-05T22:01:45,856 directory, all directories are treated like packages. 2024-08-05T22:01:45,856 ******************************************************************************** 2024-08-05T22:01:45,856 !! 2024-08-05T22:01:45,856 check.warn(importable) 2024-08-05T22:01:45,856 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2024-08-05T22:01:45,857 !! 2024-08-05T22:01:45,857 ******************************************************************************** 2024-08-05T22:01:45,857 ############################ 2024-08-05T22:01:45,857 # Package would be ignored # 2024-08-05T22:01:45,857 ############################ 2024-08-05T22:01:45,857 Python recognizes 'uncalled4.models' as an importable package[^1], 2024-08-05T22:01:45,857 but it is absent from setuptools' `packages` configuration. 2024-08-05T22:01:45,858 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T22:01:45,858 package, please make sure that 'uncalled4.models' is explicitly added 2024-08-05T22:01:45,858 to the `packages` configuration field. 2024-08-05T22:01:45,858 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T22:01:45,858 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T22:01:45,858 instead of `find_packages(...)`/`find:`). 2024-08-05T22:01:45,858 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T22:01:45,859 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T22:01:45,859 If you don't want 'uncalled4.models' to be distributed and are 2024-08-05T22:01:45,859 already explicitly excluding 'uncalled4.models' via 2024-08-05T22:01:45,859 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T22:01:45,859 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T22:01:45,859 combination with a more fine grained `package-data` configuration. 2024-08-05T22:01:45,860 You can read more about "package data files" on setuptools documentation page: 2024-08-05T22:01:45,860 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T22:01:45,860 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T22:01:45,860 even if it does not contain any `.py` files. 2024-08-05T22:01:45,860 On the other hand, currently there is no concept of package data 2024-08-05T22:01:45,861 directory, all directories are treated like packages. 2024-08-05T22:01:45,861 ******************************************************************************** 2024-08-05T22:01:45,861 !! 2024-08-05T22:01:45,861 check.warn(importable) 2024-08-05T22:01:45,861 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2024-08-05T22:01:45,861 !! 2024-08-05T22:01:45,861 ******************************************************************************** 2024-08-05T22:01:45,862 ############################ 2024-08-05T22:01:45,862 # Package would be ignored # 2024-08-05T22:01:45,862 ############################ 2024-08-05T22:01:45,862 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2024-08-05T22:01:45,862 but it is absent from setuptools' `packages` configuration. 2024-08-05T22:01:45,862 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T22:01:45,862 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2024-08-05T22:01:45,863 to the `packages` configuration field. 2024-08-05T22:01:45,863 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T22:01:45,863 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T22:01:45,863 instead of `find_packages(...)`/`find:`). 2024-08-05T22:01:45,863 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T22:01:45,864 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T22:01:45,864 If you don't want 'uncalled4.models.tombo' to be distributed and are 2024-08-05T22:01:45,864 already explicitly excluding 'uncalled4.models.tombo' via 2024-08-05T22:01:45,864 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T22:01:45,864 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T22:01:45,864 combination with a more fine grained `package-data` configuration. 2024-08-05T22:01:45,865 You can read more about "package data files" on setuptools documentation page: 2024-08-05T22:01:45,865 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T22:01:45,865 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T22:01:45,865 even if it does not contain any `.py` files. 2024-08-05T22:01:45,865 On the other hand, currently there is no concept of package data 2024-08-05T22:01:45,866 directory, all directories are treated like packages. 2024-08-05T22:01:45,866 ******************************************************************************** 2024-08-05T22:01:45,866 !! 2024-08-05T22:01:45,866 check.warn(importable) 2024-08-05T22:01:45,866 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2024-08-05T22:01:45,866 !! 2024-08-05T22:01:45,867 ******************************************************************************** 2024-08-05T22:01:45,867 ############################ 2024-08-05T22:01:45,867 # Package would be ignored # 2024-08-05T22:01:45,867 ############################ 2024-08-05T22:01:45,867 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2024-08-05T22:01:45,867 but it is absent from setuptools' `packages` configuration. 2024-08-05T22:01:45,867 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T22:01:45,868 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2024-08-05T22:01:45,868 to the `packages` configuration field. 2024-08-05T22:01:45,868 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T22:01:45,868 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T22:01:45,868 instead of `find_packages(...)`/`find:`). 2024-08-05T22:01:45,868 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T22:01:45,869 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T22:01:45,869 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2024-08-05T22:01:45,869 already explicitly excluding 'uncalled4.stats.__pycache__' via 2024-08-05T22:01:45,869 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T22:01:45,869 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T22:01:45,869 combination with a more fine grained `package-data` configuration. 2024-08-05T22:01:45,870 You can read more about "package data files" on setuptools documentation page: 2024-08-05T22:01:45,870 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T22:01:45,870 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T22:01:45,870 even if it does not contain any `.py` files. 2024-08-05T22:01:45,871 On the other hand, currently there is no concept of package data 2024-08-05T22:01:45,871 directory, all directories are treated like packages. 2024-08-05T22:01:45,871 ******************************************************************************** 2024-08-05T22:01:45,871 !! 2024-08-05T22:01:45,871 check.warn(importable) 2024-08-05T22:01:45,871 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2024-08-05T22:01:45,872 !! 2024-08-05T22:01:45,872 ******************************************************************************** 2024-08-05T22:01:45,872 ############################ 2024-08-05T22:01:45,872 # Package would be ignored # 2024-08-05T22:01:45,872 ############################ 2024-08-05T22:01:45,872 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2024-08-05T22:01:45,872 but it is absent from setuptools' `packages` configuration. 2024-08-05T22:01:45,873 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T22:01:45,873 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2024-08-05T22:01:45,873 to the `packages` configuration field. 2024-08-05T22:01:45,873 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T22:01:45,873 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T22:01:45,873 instead of `find_packages(...)`/`find:`). 2024-08-05T22:01:45,874 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T22:01:45,874 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T22:01:45,874 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2024-08-05T22:01:45,874 already explicitly excluding 'uncalled4.vis.__pycache__' via 2024-08-05T22:01:45,874 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T22:01:45,875 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T22:01:45,875 combination with a more fine grained `package-data` configuration. 2024-08-05T22:01:45,875 You can read more about "package data files" on setuptools documentation page: 2024-08-05T22:01:45,875 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T22:01:45,876 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T22:01:45,876 even if it does not contain any `.py` files. 2024-08-05T22:01:45,876 On the other hand, currently there is no concept of package data 2024-08-05T22:01:45,876 directory, all directories are treated like packages. 2024-08-05T22:01:45,876 ******************************************************************************** 2024-08-05T22:01:45,876 !! 2024-08-05T22:01:45,876 check.warn(importable) 2024-08-05T22:01:45,877 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2024-08-05T22:01:45,877 !! 2024-08-05T22:01:45,877 ******************************************************************************** 2024-08-05T22:01:45,877 ############################ 2024-08-05T22:01:45,877 # Package would be ignored # 2024-08-05T22:01:45,877 ############################ 2024-08-05T22:01:45,877 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2024-08-05T22:01:45,878 but it is absent from setuptools' `packages` configuration. 2024-08-05T22:01:45,878 This leads to an ambiguous overall configuration. If you want to distribute this 2024-08-05T22:01:45,878 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2024-08-05T22:01:45,878 to the `packages` configuration field. 2024-08-05T22:01:45,878 Alternatively, you can also rely on setuptools' discovery methods 2024-08-05T22:01:45,878 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-08-05T22:01:45,879 instead of `find_packages(...)`/`find:`). 2024-08-05T22:01:45,879 You can read more about "package discovery" on setuptools documentation page: 2024-08-05T22:01:45,879 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-08-05T22:01:45,879 If you don't want 'uncalled4.vis.assets' to be distributed and are 2024-08-05T22:01:45,879 already explicitly excluding 'uncalled4.vis.assets' via 2024-08-05T22:01:45,880 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-08-05T22:01:45,880 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-08-05T22:01:45,880 combination with a more fine grained `package-data` configuration. 2024-08-05T22:01:45,880 You can read more about "package data files" on setuptools documentation page: 2024-08-05T22:01:45,880 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-08-05T22:01:45,881 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-08-05T22:01:45,881 even if it does not contain any `.py` files. 2024-08-05T22:01:45,881 On the other hand, currently there is no concept of package data 2024-08-05T22:01:45,881 directory, all directories are treated like packages. 2024-08-05T22:01:45,881 ******************************************************************************** 2024-08-05T22:01:45,881 !! 2024-08-05T22:01:45,882 check.warn(importable) 2024-08-05T22:01:45,882 creating build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,882 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,882 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,882 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,882 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,882 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,883 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,883 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,883 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,883 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,884 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,886 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,888 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,890 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,892 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,895 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,897 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,899 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,901 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,904 copying src/uncalled4/__pycache__/train.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-08-05T22:01:45,906 creating build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-08-05T22:01:45,907 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-08-05T22:01:45,909 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-08-05T22:01:45,991 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer_sh3.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-08-05T22:01:46,078 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-08-05T22:01:46,081 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-08-05T22:01:46,084 copying src/uncalled4/models/rna004_130bps_9mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-08-05T22:01:46,117 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-08-05T22:01:46,119 creating build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-08-05T22:01:46,120 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-08-05T22:01:46,123 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-08-05T22:01:46,126 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,127 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,129 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,131 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,133 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,136 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,138 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,141 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,143 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,146 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,149 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,150 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,153 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,155 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,157 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,160 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-08-05T22:01:46,162 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-08-05T22:01:46,163 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-08-05T22:01:46,165 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-08-05T22:01:46,167 creating build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,168 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,170 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,173 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,175 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,177 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,179 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,181 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,184 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,186 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,189 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-08-05T22:01:46,191 creating build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,192 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,194 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,196 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,198 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,200 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,202 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,204 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,206 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,208 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,210 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,212 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,214 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,216 copying src/uncalled4/stats/__pycache__/readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,218 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,220 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-08-05T22:01:46,225 running build_ext 2024-08-05T22:01:46,746 building '_uncalled4' extension 2024-08-05T22:01:46,767 creating build/temp.linux-armv7l-cpython-39 2024-08-05T22:01:46,768 creating build/temp.linux-armv7l-cpython-39/src 2024-08-05T22:01:46,769 creating build/temp.linux-armv7l-cpython-39/src/cpp 2024-08-05T22:01:46,770 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/config.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/config.o -std=c++11 -O3 -g 2024-08-05T22:01:51,797 In file included from src/cpp/dtw.hpp:7, 2024-08-05T22:01:51,797 from src/cpp/config.hpp:30, 2024-08-05T22:01:51,797 from src/cpp/config.cpp:1: 2024-08-05T22:01:51,797 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:01:51,797 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T22:01:51,798 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:01:51,798 192 | struct PyArray { 2024-08-05T22:01:51,798 | ^~~~~~~ 2024-08-05T22:01:52,001 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:01:52,001 src/cpp/read_buffer.hpp:99:38: required from here 2024-08-05T22:01:52,001 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:01:52,084 In file included from src/cpp/aln.hpp:11, 2024-08-05T22:01:52,084 from src/cpp/dtw.hpp:9, 2024-08-05T22:01:52,084 from src/cpp/config.hpp:30, 2024-08-05T22:01:52,084 from src/cpp/config.cpp:1: 2024-08-05T22:01:52,084 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-08-05T22:01:52,084 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:01:52,085 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-08-05T22:01:52,085 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-08-05T22:01:52,085 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:01:52,086 65 | while (i < events.size() && events[i].start < c.end) { 2024-08-05T22:01:52,111 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-08-05T22:01:52,112 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] 2024-08-05T22:01:52,112 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-08-05T22:01:52,112 | ~~^~~~~~~~~~ 2024-08-05T22:01:52,113 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-08-05T22:01:52,113 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] 2024-08-05T22:01:52,113 158 | normalize({0, events.size(), scale, shift}); 2024-08-05T22:01:52,113 | ~~~~~~~~~~~^~ 2024-08-05T22:01:52,157 In file included from src/cpp/dtw.hpp:7, 2024-08-05T22:01:52,157 from src/cpp/config.hpp:30, 2024-08-05T22:01:52,157 from src/cpp/config.cpp:1: 2024-08-05T22:01:52,157 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:01:52,158 src/cpp/event_detector.hpp:222:39: required from here 2024-08-05T22:01:52,158 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:01:52,158 192 | struct PyArray { 2024-08-05T22:01:52,158 | ^~~~~~~ 2024-08-05T22:01:52,252 In file included from src/cpp/dtw.hpp:9, 2024-08-05T22:01:52,252 from src/cpp/config.hpp:30, 2024-08-05T22:01:52,252 from src/cpp/config.cpp:1: 2024-08-05T22:01:52,252 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-08-05T22:01:52,252 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-08-05T22:01:52,252 188 | i64 ref; 2024-08-05T22:01:52,252 | ^~~ 2024-08-05T22:01:52,257 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-08-05T22:01:52,257 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-08-05T22:01:52,257 280 | int len,dist; 2024-08-05T22:01:52,257 | ^~~~ 2024-08-05T22:01:52,268 In file included from src/cpp/dtw.hpp:7, 2024-08-05T22:01:52,269 from src/cpp/config.hpp:30, 2024-08-05T22:01:52,269 from src/cpp/config.cpp:1: 2024-08-05T22:01:52,269 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:01:52,269 src/cpp/aln.hpp:385:23: required from here 2024-08-05T22:01:52,269 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:01:52,269 192 | struct PyArray { 2024-08-05T22:01:52,269 | ^~~~~~~ 2024-08-05T22:01:52,368 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:01:52,369 src/cpp/dtw.hpp:395:26: required from here 2024-08-05T22:01:52,369 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:02:08,841 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/dtw.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/dtw.o -std=c++11 -O3 -g 2024-08-05T22:02:13,821 In file included from src/cpp/dtw.hpp:7, 2024-08-05T22:02:13,821 from src/cpp/dtw.cpp:1: 2024-08-05T22:02:13,821 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:02:13,822 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T22:02:13,822 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:02:13,822 192 | struct PyArray { 2024-08-05T22:02:13,822 | ^~~~~~~ 2024-08-05T22:02:14,023 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:02:14,023 src/cpp/read_buffer.hpp:99:38: required from here 2024-08-05T22:02:14,023 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:02:14,104 In file included from src/cpp/aln.hpp:11, 2024-08-05T22:02:14,105 from src/cpp/dtw.hpp:9, 2024-08-05T22:02:14,105 from src/cpp/dtw.cpp:1: 2024-08-05T22:02:14,105 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-08-05T22:02:14,105 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:02:14,105 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-08-05T22:02:14,106 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-08-05T22:02:14,106 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:02:14,106 65 | while (i < events.size() && events[i].start < c.end) { 2024-08-05T22:02:14,131 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-08-05T22:02:14,131 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] 2024-08-05T22:02:14,131 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-08-05T22:02:14,132 | ~~^~~~~~~~~~ 2024-08-05T22:02:14,132 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-08-05T22:02:14,132 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] 2024-08-05T22:02:14,132 158 | normalize({0, events.size(), scale, shift}); 2024-08-05T22:02:14,133 | ~~~~~~~~~~~^~ 2024-08-05T22:02:14,174 In file included from src/cpp/dtw.hpp:7, 2024-08-05T22:02:14,175 from src/cpp/dtw.cpp:1: 2024-08-05T22:02:14,175 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:02:14,175 src/cpp/event_detector.hpp:222:39: required from here 2024-08-05T22:02:14,175 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:02:14,175 192 | struct PyArray { 2024-08-05T22:02:14,175 | ^~~~~~~ 2024-08-05T22:02:14,268 In file included from src/cpp/dtw.hpp:9, 2024-08-05T22:02:14,268 from src/cpp/dtw.cpp:1: 2024-08-05T22:02:14,268 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-08-05T22:02:14,268 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-08-05T22:02:14,269 188 | i64 ref; 2024-08-05T22:02:14,269 | ^~~ 2024-08-05T22:02:14,272 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-08-05T22:02:14,272 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-08-05T22:02:14,273 280 | int len,dist; 2024-08-05T22:02:14,273 | ^~~~ 2024-08-05T22:02:14,283 In file included from src/cpp/dtw.hpp:7, 2024-08-05T22:02:14,283 from src/cpp/dtw.cpp:1: 2024-08-05T22:02:14,283 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:02:14,283 src/cpp/aln.hpp:385:23: required from here 2024-08-05T22:02:14,284 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:02:14,284 192 | struct PyArray { 2024-08-05T22:02:14,284 | ^~~~~~~ 2024-08-05T22:02:14,381 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:02:14,381 src/cpp/dtw.hpp:395:26: required from here 2024-08-05T22:02:14,381 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:02:14,400 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2024-08-05T22:02:14,401 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2024-08-05T22:02:14,401 21 | size_t i = 0, j = 0, b = 0; 2024-08-05T22:02:14,401 | ^ 2024-08-05T22:02:14,405 In file included from src/cpp/dtw.hpp:7, 2024-08-05T22:02:14,405 from src/cpp/dtw.cpp:1: 2024-08-05T22:02:14,406 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:02:14,407 src/cpp/dtw.cpp:64:30: required from here 2024-08-05T22:02:14,407 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:02:14,407 192 | struct PyArray { 2024-08-05T22:02:14,407 | ^~~~~~~ 2024-08-05T22:02:14,413 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2024-08-05T22:02:14,413 src/cpp/dtw.cpp:99:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2024-08-05T22:02:14,413 99 | auto fill = backfill_na ? samps : Interval(); 2024-08-05T22:02:14,414 | ^~~~ 2024-08-05T22:03:20,086 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/event_detector.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/event_detector.o -std=c++11 -O3 -g 2024-08-05T22:03:25,074 In file included from src/cpp/intervals.hpp:11, 2024-08-05T22:03:25,075 from src/cpp/event_detector.hpp:13, 2024-08-05T22:03:25,075 from src/cpp/event_detector.cpp:15: 2024-08-05T22:03:25,075 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:03:25,075 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T22:03:25,075 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:03:25,075 192 | struct PyArray { 2024-08-05T22:03:25,076 | ^~~~~~~ 2024-08-05T22:03:25,095 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:03:25,096 src/cpp/read_buffer.hpp:99:38: required from here 2024-08-05T22:03:25,096 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:03:25,182 In file included from src/cpp/event_detector.cpp:15: 2024-08-05T22:03:25,182 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-08-05T22:03:25,183 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:03:25,183 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-08-05T22:03:25,183 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-08-05T22:03:25,183 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:03:25,183 65 | while (i < events.size() && events[i].start < c.end) { 2024-08-05T22:03:25,213 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-08-05T22:03:25,214 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] 2024-08-05T22:03:25,214 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-08-05T22:03:25,214 | ~~^~~~~~~~~~ 2024-08-05T22:03:25,214 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-08-05T22:03:25,214 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] 2024-08-05T22:03:25,215 158 | normalize({0, events.size(), scale, shift}); 2024-08-05T22:03:25,215 | ~~~~~~~~~~~^~ 2024-08-05T22:03:25,274 In file included from src/cpp/intervals.hpp:11, 2024-08-05T22:03:25,274 from src/cpp/event_detector.hpp:13, 2024-08-05T22:03:25,274 from src/cpp/event_detector.cpp:15: 2024-08-05T22:03:25,274 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:03:25,275 src/cpp/event_detector.hpp:222:39: required from here 2024-08-05T22:03:25,275 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:03:25,275 192 | struct PyArray { 2024-08-05T22:03:25,275 | ^~~~~~~ 2024-08-05T22:03:25,328 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:03:25,328 src/cpp/event_detector.cpp:250:30: required from here 2024-08-05T22:03:25,328 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:03:49,387 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/intervals.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/intervals.o -std=c++11 -O3 -g 2024-08-05T22:03:54,328 In file included from src/cpp/intervals.hpp:11, 2024-08-05T22:03:54,328 from src/cpp/intervals.cpp:2: 2024-08-05T22:03:54,329 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:03:54,329 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T22:03:54,329 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:03:54,329 192 | struct PyArray { 2024-08-05T22:03:54,329 | ^~~~~~~ 2024-08-05T22:03:56,328 In file included from src/cpp/intervals.cpp:2: 2024-08-05T22:03:56,329 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2024-08-05T22:03:56,329 src/cpp/intervals.hpp:467:31: required from ‘static void IntervalIndex::pybind(pybind11::module_&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:03:56,329 src/cpp/intervals.cpp:7:25: required from here 2024-08-05T22:03:56,329 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] 2024-08-05T22:03:56,329 348 | while (gap >= MAX_LEN_I16) { 2024-08-05T22:03:56,330 | ~~~~^~~~~~~~~~~~~~ 2024-08-05T22:04:28,351 In file included from /usr/include/c++/10/vector:72, 2024-08-05T22:04:28,351 from src/cpp/intervals.hpp:6, 2024-08-05T22:04:28,351 from src/cpp/intervals.cpp:2: 2024-08-05T22:04:28,352 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Interval&}; _Tp = Interval; _Alloc = std::allocator >]’: 2024-08-05T22:04:28,352 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-08-05T22:04:28,352 426 | vector<_Tp, _Alloc>:: 2024-08-05T22:04:28,352 | ^~~~~~~~~~~~~~~~~~~ 2024-08-05T22:04:28,433 In file included from /usr/include/c++/10/vector:67, 2024-08-05T22:04:28,433 from src/cpp/intervals.hpp:6, 2024-08-05T22:04:28,434 from src/cpp/intervals.cpp:2: 2024-08-05T22:04:28,434 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::mirror() const [with T = long long int]’: 2024-08-05T22:04:28,434 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:28,434 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:28,434 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:28,500 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’: 2024-08-05T22:04:28,500 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:28,501 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:28,501 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:28,501 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:28,501 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:28,501 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:28,603 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::intersect(IntervalIndex) const [with T = long long int]’: 2024-08-05T22:04:28,603 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:28,604 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:28,604 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:28,699 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’: 2024-08-05T22:04:28,699 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:28,700 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:28,700 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:28,700 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:28,700 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:28,700 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:28,700 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:28,701 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:28,701 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:39,431 In file included from /usr/include/c++/10/vector:72, 2024-08-05T22:04:39,431 from src/cpp/intervals.hpp:6, 2024-08-05T22:04:39,432 from src/cpp/intervals.cpp:2: 2024-08-05T22:04:39,432 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: 2024-08-05T22:04:39,432 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-08-05T22:04:39,432 426 | vector<_Tp, _Alloc>:: 2024-08-05T22:04:39,432 | ^~~~~~~~~~~~~~~~~~~ 2024-08-05T22:04:39,503 /usr/include/c++/10/bits/vector.tcc: In member function ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector, std::allocator > >; Value = std::pair]’: 2024-08-05T22:04:39,503 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:39,503 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-08-05T22:04:39,504 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-08-05T22:04:39,701 In file included from /usr/include/c++/10/vector:67, 2024-08-05T22:04:39,701 from src/cpp/intervals.hpp:6, 2024-08-05T22:04:39,701 from src/cpp/intervals.cpp:2: 2024-08-05T22:04:39,701 /usr/include/c++/10/bits/stl_vector.h: In static member function ‘static pybind11::handle pybind11::cpp_function::initialize::execute >, {}, 0>::, std::allocator > >)>, void, {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}, {pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor}>::::_FUN(pybind11::detail::function_call&)’: 2024-08-05T22:04:39,701 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:39,701 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:39,702 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:39,702 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-08-05T22:04:39,702 1198 | _M_realloc_insert(end(), __x); 2024-08-05T22:04:39,702 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-08-05T22:04:49,957 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/normalizer.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/normalizer.o -std=c++11 -O3 -g 2024-08-05T22:05:00,411 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/pore_model.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/pore_model.o -std=c++11 -O3 -g 2024-08-05T22:05:05,356 In file included from src/cpp/pore_model.hpp:36, 2024-08-05T22:05:05,357 from src/cpp/pore_model.cpp:1: 2024-08-05T22:05:05,357 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:05,357 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T22:05:05,357 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:05,357 192 | struct PyArray { 2024-08-05T22:05:05,357 | ^~~~~~~ 2024-08-05T22:05:39,175 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/pybinder.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/pybinder.o -std=c++11 -O3 -g 2024-08-05T22:05:44,336 In file included from src/cpp/read_buffer.hpp:30, 2024-08-05T22:05:44,336 from src/cpp/pybinder.cpp:5: 2024-08-05T22:05:44,336 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:44,336 src/cpp/read_buffer.hpp:99:38: required from here 2024-08-05T22:05:44,337 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:44,337 192 | struct PyArray { 2024-08-05T22:05:44,337 | ^~~~~~~ 2024-08-05T22:05:44,364 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:44,364 src/cpp/intervals.hpp:110:20: required from here 2024-08-05T22:05:44,364 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:44,450 In file included from src/cpp/signal_processor.hpp:7, 2024-08-05T22:05:44,450 from src/cpp/pybinder.cpp:6: 2024-08-05T22:05:44,451 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-08-05T22:05:44,451 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:05:44,451 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-08-05T22:05:44,451 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-08-05T22:05:44,451 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:05:44,451 65 | while (i < events.size() && events[i].start < c.end) { 2024-08-05T22:05:44,481 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-08-05T22:05:44,482 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] 2024-08-05T22:05:44,482 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-08-05T22:05:44,482 | ~~^~~~~~~~~~ 2024-08-05T22:05:44,482 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-08-05T22:05:44,482 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] 2024-08-05T22:05:44,483 158 | normalize({0, events.size(), scale, shift}); 2024-08-05T22:05:44,483 | ~~~~~~~~~~~^~ 2024-08-05T22:05:44,542 In file included from src/cpp/read_buffer.hpp:30, 2024-08-05T22:05:44,542 from src/cpp/pybinder.cpp:5: 2024-08-05T22:05:44,543 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:44,543 src/cpp/event_detector.hpp:222:39: required from here 2024-08-05T22:05:44,543 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:44,543 192 | struct PyArray { 2024-08-05T22:05:44,543 | ^~~~~~~ 2024-08-05T22:05:44,792 In file included from src/cpp/dtw.hpp:9, 2024-08-05T22:05:44,792 from src/cpp/pybinder.cpp:8: 2024-08-05T22:05:44,792 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-08-05T22:05:44,792 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-08-05T22:05:44,792 188 | i64 ref; 2024-08-05T22:05:44,793 | ^~~ 2024-08-05T22:05:44,796 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-08-05T22:05:44,796 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-08-05T22:05:44,797 280 | int len,dist; 2024-08-05T22:05:44,797 | ^~~~ 2024-08-05T22:05:44,807 In file included from src/cpp/read_buffer.hpp:30, 2024-08-05T22:05:44,807 from src/cpp/pybinder.cpp:5: 2024-08-05T22:05:44,807 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:44,808 src/cpp/aln.hpp:385:23: required from here 2024-08-05T22:05:44,808 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:44,808 192 | struct PyArray { 2024-08-05T22:05:44,808 | ^~~~~~~ 2024-08-05T22:05:44,906 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:44,906 src/cpp/dtw.hpp:395:26: required from here 2024-08-05T22:05:44,906 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:44,944 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:44,944 src/cpp/eventalign.hpp:110:31: required from here 2024-08-05T22:05:44,944 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:48,344 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:48,344 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const 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]’ 2024-08-05T22:05:48,345 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]’ 2024-08-05T22:05:48,345 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:05:48,345 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:48,371 In file included from src/cpp/pybinder.cpp:10: 2024-08-05T22:05:48,371 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]’: 2024-08-05T22:05:48,371 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]’ 2024-08-05T22:05:48,371 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:05:48,372 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:05:48,372 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-08-05T22:05:48,372 | ~~^~~~~~~~~~~ 2024-08-05T22:05:48,600 In file included from src/cpp/read_buffer.hpp:30, 2024-08-05T22:05:48,601 from src/cpp/pybinder.cpp:5: 2024-08-05T22:05:48,601 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-08-05T22:05:48,601 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const 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]’ 2024-08-05T22:05:48,601 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]’ 2024-08-05T22:05:48,601 src/cpp/pybinder.cpp:67:31: required from here 2024-08-05T22:05:48,601 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-08-05T22:05:48,601 192 | struct PyArray { 2024-08-05T22:05:48,602 | ^~~~~~~ 2024-08-05T22:05:48,624 In file included from src/cpp/pybinder.cpp:10: 2024-08-05T22:05:48,625 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]’: 2024-08-05T22:05:48,625 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]’ 2024-08-05T22:05:48,625 src/cpp/pybinder.cpp:67:31: required from here 2024-08-05T22:05:48,625 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-08-05T22:05:48,625 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-08-05T22:05:48,625 | ~~^~~~~~~~~~~ 2024-08-05T22:05:54,931 In file included from src/cpp/pybinder.cpp:8: 2024-08-05T22:05:54,931 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-08-05T22:05:54,931 src/cpp/dtw.hpp:736:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:05:54,932 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]’ 2024-08-05T22:05:54,932 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:05:54,932 src/cpp/dtw.hpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-08-05T22:05:54,932 646 | if (q0 >= qry_size()) { 2024-08-05T22:05:54,932 | ~~~^~~~~~~~~~~~~ 2024-08-05T22:05:54,932 src/cpp/dtw.hpp:653:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-08-05T22:05:54,933 653 | if (r1 > ref_size()) { 2024-08-05T22:05:54,933 | ~~~^~~~~~~~~~~~ 2024-08-05T22:05:55,504 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-08-05T22:05:55,504 src/cpp/dtw.hpp:736:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:05:55,504 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]’ 2024-08-05T22:05:55,505 src/cpp/pybinder.cpp:67:31: required from here 2024-08-05T22:05:55,505 src/cpp/dtw.hpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-08-05T22:05:55,505 646 | if (q0 >= qry_size()) { 2024-08-05T22:05:55,505 | ~~~^~~~~~~~~~~~~ 2024-08-05T22:05:55,505 src/cpp/dtw.hpp:653:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-08-05T22:05:55,505 653 | if (r1 > ref_size()) { 2024-08-05T22:05:55,506 | ~~~^~~~~~~~~~~~ 2024-08-05T22:06:05,832 In file included from src/cpp/seq.hpp:32, 2024-08-05T22:06:05,832 from src/cpp/pybinder.cpp:7: 2024-08-05T22:06:05,832 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]’: 2024-08-05T22:06:05,832 src/cpp/pore_model.hpp:505:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:05,833 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:05,833 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:05,833 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]’ 2024-08-05T22:06:05,833 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:06:05,833 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-08-05T22:06:05,833 516 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2024-08-05T22:06:05,834 | ~~~~~~~~~~^ 2024-08-05T22:06:05,834 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]’: 2024-08-05T22:06:05,834 src/cpp/pore_model.hpp:507:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:05,834 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:05,834 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:05,834 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]’ 2024-08-05T22:06:05,835 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:06:05,835 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-08-05T22:06:10,393 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]’: 2024-08-05T22:06:10,393 src/cpp/pore_model.hpp:505:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:10,393 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:10,393 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:10,393 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]’ 2024-08-05T22:06:10,394 src/cpp/pybinder.cpp:67:31: required from here 2024-08-05T22:06:10,394 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-08-05T22:06:10,394 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]’: 2024-08-05T22:06:10,394 src/cpp/pore_model.hpp:507:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:10,394 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:10,394 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:10,395 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]’ 2024-08-05T22:06:10,395 src/cpp/pybinder.cpp:67:31: required from here 2024-08-05T22:06:10,395 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-08-05T22:06:15,065 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]’: 2024-08-05T22:06:15,065 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-08-05T22:06:15,065 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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]’ 2024-08-05T22:06:15,065 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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}]’ 2024-08-05T22:06:15,066 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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 = {}]’ 2024-08-05T22:06:15,066 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:15,066 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]’ 2024-08-05T22:06:15,066 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:06:15,066 src/cpp/pore_model.hpp:355:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-08-05T22:06:15,066 355 | auto get_kmer = [&](size_t i) {return i;}; 2024-08-05T22:06:15,067 | ^~~~~~~~ 2024-08-05T22:06:15,793 In file included from src/cpp/pybinder.cpp:8: 2024-08-05T22:06:15,793 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-08-05T22:06:15,793 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]’ 2024-08-05T22:06:15,794 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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]’ 2024-08-05T22:06:15,794 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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&}]’ 2024-08-05T22:06:15,794 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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 = {}]’ 2024-08-05T22:06:15,794 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:15,794 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]’ 2024-08-05T22:06:15,794 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:06:15,795 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] 2024-08-05T22:06:15,795 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-08-05T22:06:15,795 | ~~^~~~~~~~~~~~ 2024-08-05T22:06:15,796 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-08-05T22:06:15,796 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]’ 2024-08-05T22:06:15,797 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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]’ 2024-08-05T22:06:15,797 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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&}]’ 2024-08-05T22:06:15,797 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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 = {}]’ 2024-08-05T22:06:15,797 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:15,797 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]’ 2024-08-05T22:06:15,797 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:06:15,798 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] 2024-08-05T22:06:15,798 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-08-05T22:06:15,798 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-08-05T22:06:17,100 In file included from src/cpp/seq.hpp:32, 2024-08-05T22:06:17,100 from src/cpp/pybinder.cpp:7: 2024-08-05T22:06:17,100 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]’: 2024-08-05T22:06:17,101 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2024-08-05T22:06:17,101 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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]’ 2024-08-05T22:06:17,101 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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}]’ 2024-08-05T22:06:17,101 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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 = {}]’ 2024-08-05T22:06:17,101 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:17,101 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]’ 2024-08-05T22:06:17,102 src/cpp/pybinder.cpp:67:31: required from here 2024-08-05T22:06:17,102 src/cpp/pore_model.hpp:355:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-08-05T22:06:17,102 355 | auto get_kmer = [&](size_t i) {return i;}; 2024-08-05T22:06:17,102 | ^~~~~~~~ 2024-08-05T22:06:17,260 In file included from src/cpp/pybinder.cpp:8: 2024-08-05T22:06:17,260 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-08-05T22:06:17,260 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]’ 2024-08-05T22:06:17,260 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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]’ 2024-08-05T22:06:17,260 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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&}]’ 2024-08-05T22:06:17,260 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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 = {}]’ 2024-08-05T22:06:17,261 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:17,261 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]’ 2024-08-05T22:06:17,261 src/cpp/pybinder.cpp:67:31: required from here 2024-08-05T22:06:17,261 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] 2024-08-05T22:06:17,261 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-08-05T22:06:17,261 | ~~^~~~~~~~~~~~ 2024-08-05T22:06:17,263 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-08-05T22:06:17,263 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]’ 2024-08-05T22:06:17,263 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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]’ 2024-08-05T22:06:17,263 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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&}]’ 2024-08-05T22:06:17,263 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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 = {}]’ 2024-08-05T22:06:17,264 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:17,264 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]’ 2024-08-05T22:06:17,264 src/cpp/pybinder.cpp:67:31: required from here 2024-08-05T22:06:17,264 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] 2024-08-05T22:06:17,264 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-08-05T22:06:17,264 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-08-05T22:06:18,425 In file included from src/cpp/read_buffer.hpp:30, 2024-08-05T22:06:18,425 from src/cpp/pybinder.cpp:5: 2024-08-05T22:06:18,426 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2024-08-05T22:06:18,426 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]’ 2024-08-05T22:06:18,426 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-08-05T22:06:18,426 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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]’ 2024-08-05T22:06:18,426 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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}]’ 2024-08-05T22:06:18,426 /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/.eggs/pybind11-2.13.1-py3.9.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 = {}]’ 2024-08-05T22:06:18,426 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-08-05T22:06:18,427 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]’ 2024-08-05T22:06:18,427 src/cpp/pybinder.cpp:66:31: required from here 2024-08-05T22:06:18,427 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2024-08-05T22:06:18,427 144 | auto sum = super::sum(); 2024-08-05T22:06:18,427 | ^~~ 2024-08-05T22:06:18,427 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2024-08-05T22:06:18,427 145 | auto len = super::size(); 2024-08-05T22:06:18,427 | ^~~ 2024-08-05T22:06:32,945 virtual memory exhausted: Cannot allocate memory 2024-08-05T22:06:33,067 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-08-05T22:06:33,204 ERROR: python setup.py bdist_wheel exited with 1 2024-08-05T22:06:33,221 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2024-08-05T22:06:33,221 exec(compile('"'"''"'"''"'"' 2024-08-05T22:06:33,221 # This is -- a caller that pip uses to run setup.py 2024-08-05T22:06:33,221 # 2024-08-05T22:06:33,221 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-08-05T22:06:33,221 # import from `distutils.core` to work with newer packaging standards. 2024-08-05T22:06:33,221 # - It provides a clear error message when setuptools is not installed. 2024-08-05T22:06:33,221 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-08-05T22:06:33,221 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-08-05T22:06:33,221 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-08-05T22:06:33,221 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-08-05T22:06:33,221 import os, sys, tokenize 2024-08-05T22:06:33,221 2024-08-05T22:06:33,221 try: 2024-08-05T22:06:33,221 import setuptools 2024-08-05T22:06:33,221 except ImportError as error: 2024-08-05T22:06:33,221 print( 2024-08-05T22:06:33,221 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-08-05T22:06:33,221 "the build environment.", 2024-08-05T22:06:33,221 file=sys.stderr, 2024-08-05T22:06:33,221 ) 2024-08-05T22:06:33,221 sys.exit(1) 2024-08-05T22:06:33,221 2024-08-05T22:06:33,221 __file__ = %r 2024-08-05T22:06:33,221 sys.argv[0] = __file__ 2024-08-05T22:06:33,221 2024-08-05T22:06:33,221 if os.path.exists(__file__): 2024-08-05T22:06:33,221 filename = __file__ 2024-08-05T22:06:33,221 with tokenize.open(__file__) as f: 2024-08-05T22:06:33,221 setup_py_code = f.read() 2024-08-05T22:06:33,221 else: 2024-08-05T22:06:33,221 filename = "" 2024-08-05T22:06:33,221 setup_py_code = "from setuptools import setup; setup()" 2024-08-05T22:06:33,221 2024-08-05T22:06:33,221 exec(compile(setup_py_code, filename, "exec")) 2024-08-05T22:06:33,221 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ygakpr6p[/] 2024-08-05T22:06:33,222 [bold magenta]cwd[/]: /tmp/pip-wheel-firjgvdh/uncalled4_96d51e04adc84e3bb489f06c408a2575/ 2024-08-05T22:06:33,222 Building wheel for uncalled4 (setup.py): finished with status 'error' 2024-08-05T22:06:33,223 ERROR: Failed building wheel for uncalled4 2024-08-05T22:06:33,224 Running setup.py clean for uncalled4 2024-08-05T22:06:33,224 Running command python setup.py clean 2024-08-05T22:06:34,213 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:85: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-08-05T22:06:34,213 !! 2024-08-05T22:06:34,214 ******************************************************************************** 2024-08-05T22:06:34,214 Requirements should be satisfied by a PEP 517 installer. 2024-08-05T22:06:34,214 If you are using pip, you can try `pip install --use-pep517`. 2024-08-05T22:06:34,214 ******************************************************************************** 2024-08-05T22:06:34,214 !! 2024-08-05T22:06:34,214 dist.fetch_build_eggs(dist.setup_requires) 2024-08-05T22:06:34,433 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'build_backend' 2024-08-05T22:06:34,433 warnings.warn(msg) 2024-08-05T22:06:34,599 running clean 2024-08-05T22:06:34,653 removing 'build/temp.linux-armv7l-cpython-39' (and everything under it) 2024-08-05T22:06:34,669 removing 'build/lib.linux-armv7l-cpython-39' (and everything under it) 2024-08-05T22:06:34,701 'build/bdist.linux-armv7l' does not exist -- can't clean it 2024-08-05T22:06:34,701 'build/scripts-3.9' does not exist -- can't clean it 2024-08-05T22:06:34,702 removing 'build' 2024-08-05T22:06:34,798 Failed to build uncalled4 2024-08-05T22:06:34,800 ERROR: Failed to build one or more wheels 2024-08-05T22:06:34,801 Exception information: 2024-08-05T22:06:34,801 Traceback (most recent call last): 2024-08-05T22:06:34,801 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 179, in exc_logging_wrapper 2024-08-05T22:06:34,801 status = run_func(*args) 2024-08-05T22:06:34,801 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 67, in wrapper 2024-08-05T22:06:34,801 return func(self, options, args) 2024-08-05T22:06:34,801 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2024-08-05T22:06:34,801 raise CommandError("Failed to build one or more wheels") 2024-08-05T22:06:34,801 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-08-05T22:06:34,804 Removed build tracker: '/tmp/pip-build-tracker-g94lcvgj'