2025-09-14T11:43:00,848 Created temporary directory: /tmp/pip-build-tracker-wmy651m9 2025-09-14T11:43:00,849 Initialized build tracking at /tmp/pip-build-tracker-wmy651m9 2025-09-14T11:43:00,849 Created build tracker: /tmp/pip-build-tracker-wmy651m9 2025-09-14T11:43:00,849 Entered build tracker: /tmp/pip-build-tracker-wmy651m9 2025-09-14T11:43:00,849 Created temporary directory: /tmp/pip-wheel-xrmh8qzq 2025-09-14T11:43:00,853 Created temporary directory: /tmp/pip-ephem-wheel-cache-96f1dr_g 2025-09-14T11:43:00,912 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-14T11:43:00,914 2 location(s) to search for versions of uncalled4: 2025-09-14T11:43:00,914 * https://pypi.org/simple/uncalled4/ 2025-09-14T11:43:00,914 * https://www.piwheels.org/simple/uncalled4/ 2025-09-14T11:43:00,915 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2025-09-14T11:43:00,915 Getting page https://pypi.org/simple/uncalled4/ 2025-09-14T11:43:00,916 Found index url https://pypi.org/simple/ 2025-09-14T11:43:00,986 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2025-09-14T11:43:00,987 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 2025-09-14T11:43:00,988 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 2025-09-14T11:43:00,988 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 2025-09-14T11:43:00,988 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 2025-09-14T11:43:00,988 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2025-09-14T11:43:00,989 Getting page https://www.piwheels.org/simple/uncalled4/ 2025-09-14T11:43:00,990 Found index url https://www.piwheels.org/simple/ 2025-09-14T11:43:01,083 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2025-09-14T11:43:01,084 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2025-09-14T11:43:01,084 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2025-09-14T11:43:01,109 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2025-09-14T11:43:01,111 Collecting uncalled4==4.1.0 2025-09-14T11:43:01,112 Created temporary directory: /tmp/pip-unpack-7s3j21dc 2025-09-14T11:43:01,255 Downloading uncalled4-4.1.0.tar.gz (25.8 MB) 2025-09-14T11:43:06,382 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-wmy651m9' 2025-09-14T11:43:06,383 Running setup.py (path:/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/setup.py) egg_info for package uncalled4 2025-09-14T11:43:06,384 Created temporary directory: /tmp/pip-pip-egg-info-oqkmo1is 2025-09-14T11:43:06,384 Preparing metadata (setup.py): started 2025-09-14T11:43:06,385 Running command python setup.py egg_info 2025-09-14T11:43:07,211 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-14T11:43:07,211 !! 2025-09-14T11:43:07,211 ******************************************************************************** 2025-09-14T11:43:07,211 Requirements should be satisfied by a PEP 517 installer. 2025-09-14T11:43:07,211 If you are using pip, you can try `pip install --use-pep517`. 2025-09-14T11:43:07,211 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-14T11:43:07,212 or your builds will no longer be supported. 2025-09-14T11:43:07,212 ******************************************************************************** 2025-09-14T11:43:07,212 !! 2025-09-14T11:43:07,212 dist.fetch_build_eggs(dist.setup_requires) 2025-09-14T11:43:10,025 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'build_backend' 2025-09-14T11:43:10,026 warnings.warn(msg) 2025-09-14T11:43:10,261 running egg_info 2025-09-14T11:43:10,339 creating /tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info 2025-09-14T11:43:10,339 writing /tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info/PKG-INFO 2025-09-14T11:43:10,340 writing dependency_links to /tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info/dependency_links.txt 2025-09-14T11:43:10,341 writing entry points to /tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info/entry_points.txt 2025-09-14T11:43:10,342 writing requirements to /tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info/requires.txt 2025-09-14T11:43:10,342 writing top-level names to /tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info/top_level.txt 2025-09-14T11:43:10,342 writing manifest file '/tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info/SOURCES.txt' 2025-09-14T11:43:10,646 reading manifest file '/tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info/SOURCES.txt' 2025-09-14T11:43:10,647 reading manifest template 'MANIFEST.in' 2025-09-14T11:43:10,657 adding license file 'LICENSE' 2025-09-14T11:43:10,663 writing manifest file '/tmp/pip-pip-egg-info-oqkmo1is/uncalled4.egg-info/SOURCES.txt' 2025-09-14T11:43:10,777 Preparing metadata (setup.py): finished with status 'done' 2025-09-14T11:43:10,782 Source in /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a 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 2025-09-14T11:43:10,782 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-wmy651m9' 2025-09-14T11:43:10,789 Created temporary directory: /tmp/pip-unpack-ote30fws 2025-09-14T11:43:10,790 Created temporary directory: /tmp/pip-unpack-uvxv0a3m 2025-09-14T11:43:10,790 Building wheels for collected packages: uncalled4 2025-09-14T11:43:10,791 Created temporary directory: /tmp/pip-wheel-_2gmue6v 2025-09-14T11:43:10,792 DEPRECATION: Building 'uncalled4' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'uncalled4'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-14T11:43:10,793 Building wheel for uncalled4 (setup.py): started 2025-09-14T11:43:10,794 Destination directory: /tmp/pip-wheel-_2gmue6v 2025-09-14T11:43:10,794 Running command python setup.py bdist_wheel 2025-09-14T11:43:11,603 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-14T11:43:11,603 !! 2025-09-14T11:43:11,603 ******************************************************************************** 2025-09-14T11:43:11,603 Requirements should be satisfied by a PEP 517 installer. 2025-09-14T11:43:11,603 If you are using pip, you can try `pip install --use-pep517`. 2025-09-14T11:43:11,604 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-14T11:43:11,604 or your builds will no longer be supported. 2025-09-14T11:43:11,604 ******************************************************************************** 2025-09-14T11:43:11,604 !! 2025-09-14T11:43:11,604 dist.fetch_build_eggs(dist.setup_requires) 2025-09-14T11:43:12,102 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'build_backend' 2025-09-14T11:43:12,102 warnings.warn(msg) 2025-09-14T11:43:12,298 running bdist_wheel 2025-09-14T11:43:12,671 running build 2025-09-14T11:43:12,671 running build_py 2025-09-14T11:43:12,748 creating build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,749 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,749 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,750 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,751 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,751 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,752 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,752 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,753 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,753 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,754 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,754 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,755 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,756 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,756 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-313/uncalled4 2025-09-14T11:43:12,757 creating build/lib.linux-armv7l-cpython-313/uncalled4/vis 2025-09-14T11:43:12,757 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-313/uncalled4/vis 2025-09-14T11:43:12,758 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-313/uncalled4/vis 2025-09-14T11:43:12,758 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-313/uncalled4/vis 2025-09-14T11:43:12,759 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-313/uncalled4/vis 2025-09-14T11:43:12,759 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-313/uncalled4/vis 2025-09-14T11:43:12,760 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-313/uncalled4/vis 2025-09-14T11:43:12,761 creating build/lib.linux-armv7l-cpython-313/uncalled4/stats 2025-09-14T11:43:12,761 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-313/uncalled4/stats 2025-09-14T11:43:12,761 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-313/uncalled4/stats 2025-09-14T11:43:12,762 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-313/uncalled4/stats 2025-09-14T11:43:12,763 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-313/uncalled4/stats 2025-09-14T11:43:12,763 creating build/lib.linux-armv7l-cpython-313/uncalled4/io 2025-09-14T11:43:12,764 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-313/uncalled4/io 2025-09-14T11:43:12,764 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-313/uncalled4/io 2025-09-14T11:43:12,765 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-313/uncalled4/io 2025-09-14T11:43:12,765 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-313/uncalled4/io 2025-09-14T11:43:12,766 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-313/uncalled4/io 2025-09-14T11:43:12,766 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-313/uncalled4/io 2025-09-14T11:43:12,767 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-313/uncalled4/io 2025-09-14T11:43:12,767 running egg_info 2025-09-14T11:43:12,844 writing src/uncalled4.egg-info/PKG-INFO 2025-09-14T11:43:12,845 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2025-09-14T11:43:12,846 writing entry points to src/uncalled4.egg-info/entry_points.txt 2025-09-14T11:43:12,846 writing requirements to src/uncalled4.egg-info/requires.txt 2025-09-14T11:43:12,847 writing top-level names to src/uncalled4.egg-info/top_level.txt 2025-09-14T11:43:12,926 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2025-09-14T11:43:12,933 reading manifest template 'MANIFEST.in' 2025-09-14T11:43:12,943 adding license file 'LICENSE' 2025-09-14T11:43:12,951 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2025-09-14T11:43:12,953 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2025-09-14T11:43:12,953 !! 2025-09-14T11:43:12,953 ******************************************************************************** 2025-09-14T11:43:12,953 ############################ 2025-09-14T11:43:12,953 # Package would be ignored # 2025-09-14T11:43:12,953 ############################ 2025-09-14T11:43:12,953 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2025-09-14T11:43:12,953 but it is absent from setuptools' `packages` configuration. 2025-09-14T11:43:12,954 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T11:43:12,954 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2025-09-14T11:43:12,954 to the `packages` configuration field. 2025-09-14T11:43:12,954 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T11:43:12,954 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T11:43:12,954 instead of `find_packages(...)`/`find:`). 2025-09-14T11:43:12,954 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T11:43:12,954 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T11:43:12,955 If you don't want 'uncalled4.__pycache__' to be distributed and are 2025-09-14T11:43:12,955 already explicitly excluding 'uncalled4.__pycache__' via 2025-09-14T11:43:12,955 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T11:43:12,955 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T11:43:12,955 combination with a more fine grained `package-data` configuration. 2025-09-14T11:43:12,955 You can read more about "package data files" on setuptools documentation page: 2025-09-14T11:43:12,955 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T11:43:12,956 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T11:43:12,956 even if it does not contain any `.py` files. 2025-09-14T11:43:12,956 On the other hand, currently there is no concept of package data 2025-09-14T11:43:12,956 directory, all directories are treated like packages. 2025-09-14T11:43:12,956 ******************************************************************************** 2025-09-14T11:43:12,956 !! 2025-09-14T11:43:12,956 check.warn(importable) 2025-09-14T11:43:12,956 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2025-09-14T11:43:12,956 !! 2025-09-14T11:43:12,957 ******************************************************************************** 2025-09-14T11:43:12,957 ############################ 2025-09-14T11:43:12,957 # Package would be ignored # 2025-09-14T11:43:12,957 ############################ 2025-09-14T11:43:12,957 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2025-09-14T11:43:12,957 but it is absent from setuptools' `packages` configuration. 2025-09-14T11:43:12,957 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T11:43:12,957 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2025-09-14T11:43:12,957 to the `packages` configuration field. 2025-09-14T11:43:12,958 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T11:43:12,958 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T11:43:12,958 instead of `find_packages(...)`/`find:`). 2025-09-14T11:43:12,958 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T11:43:12,958 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T11:43:12,958 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2025-09-14T11:43:12,958 already explicitly excluding 'uncalled4.io.__pycache__' via 2025-09-14T11:43:12,958 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T11:43:12,959 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T11:43:12,959 combination with a more fine grained `package-data` configuration. 2025-09-14T11:43:12,959 You can read more about "package data files" on setuptools documentation page: 2025-09-14T11:43:12,959 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T11:43:12,959 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T11:43:12,959 even if it does not contain any `.py` files. 2025-09-14T11:43:12,959 On the other hand, currently there is no concept of package data 2025-09-14T11:43:12,960 directory, all directories are treated like packages. 2025-09-14T11:43:12,960 ******************************************************************************** 2025-09-14T11:43:12,960 !! 2025-09-14T11:43:12,960 check.warn(importable) 2025-09-14T11:43:12,960 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2025-09-14T11:43:12,960 !! 2025-09-14T11:43:12,960 ******************************************************************************** 2025-09-14T11:43:12,960 ############################ 2025-09-14T11:43:12,960 # Package would be ignored # 2025-09-14T11:43:12,961 ############################ 2025-09-14T11:43:12,961 Python recognizes 'uncalled4.models' as an importable package[^1], 2025-09-14T11:43:12,961 but it is absent from setuptools' `packages` configuration. 2025-09-14T11:43:12,961 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T11:43:12,961 package, please make sure that 'uncalled4.models' is explicitly added 2025-09-14T11:43:12,961 to the `packages` configuration field. 2025-09-14T11:43:12,961 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T11:43:12,961 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T11:43:12,961 instead of `find_packages(...)`/`find:`). 2025-09-14T11:43:12,962 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T11:43:12,962 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T11:43:12,962 If you don't want 'uncalled4.models' to be distributed and are 2025-09-14T11:43:12,962 already explicitly excluding 'uncalled4.models' via 2025-09-14T11:43:12,962 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T11:43:12,962 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T11:43:12,962 combination with a more fine grained `package-data` configuration. 2025-09-14T11:43:12,963 You can read more about "package data files" on setuptools documentation page: 2025-09-14T11:43:12,963 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T11:43:12,963 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T11:43:12,963 even if it does not contain any `.py` files. 2025-09-14T11:43:12,963 On the other hand, currently there is no concept of package data 2025-09-14T11:43:12,963 directory, all directories are treated like packages. 2025-09-14T11:43:12,963 ******************************************************************************** 2025-09-14T11:43:12,964 !! 2025-09-14T11:43:12,964 check.warn(importable) 2025-09-14T11:43:12,964 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2025-09-14T11:43:12,964 !! 2025-09-14T11:43:12,964 ******************************************************************************** 2025-09-14T11:43:12,964 ############################ 2025-09-14T11:43:12,964 # Package would be ignored # 2025-09-14T11:43:12,964 ############################ 2025-09-14T11:43:12,964 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2025-09-14T11:43:12,964 but it is absent from setuptools' `packages` configuration. 2025-09-14T11:43:12,965 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T11:43:12,965 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2025-09-14T11:43:12,965 to the `packages` configuration field. 2025-09-14T11:43:12,965 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T11:43:12,965 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T11:43:12,965 instead of `find_packages(...)`/`find:`). 2025-09-14T11:43:12,965 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T11:43:12,966 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T11:43:12,966 If you don't want 'uncalled4.models.tombo' to be distributed and are 2025-09-14T11:43:12,966 already explicitly excluding 'uncalled4.models.tombo' via 2025-09-14T11:43:12,966 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T11:43:12,966 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T11:43:12,966 combination with a more fine grained `package-data` configuration. 2025-09-14T11:43:12,966 You can read more about "package data files" on setuptools documentation page: 2025-09-14T11:43:12,966 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T11:43:12,967 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T11:43:12,967 even if it does not contain any `.py` files. 2025-09-14T11:43:12,967 On the other hand, currently there is no concept of package data 2025-09-14T11:43:12,967 directory, all directories are treated like packages. 2025-09-14T11:43:12,967 ******************************************************************************** 2025-09-14T11:43:12,967 !! 2025-09-14T11:43:12,967 check.warn(importable) 2025-09-14T11:43:12,967 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2025-09-14T11:43:12,968 !! 2025-09-14T11:43:12,968 ******************************************************************************** 2025-09-14T11:43:12,968 ############################ 2025-09-14T11:43:12,968 # Package would be ignored # 2025-09-14T11:43:12,968 ############################ 2025-09-14T11:43:12,968 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2025-09-14T11:43:12,968 but it is absent from setuptools' `packages` configuration. 2025-09-14T11:43:12,968 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T11:43:12,968 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2025-09-14T11:43:12,969 to the `packages` configuration field. 2025-09-14T11:43:12,969 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T11:43:12,969 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T11:43:12,969 instead of `find_packages(...)`/`find:`). 2025-09-14T11:43:12,969 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T11:43:12,969 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T11:43:12,969 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2025-09-14T11:43:12,969 already explicitly excluding 'uncalled4.stats.__pycache__' via 2025-09-14T11:43:12,970 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T11:43:12,970 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T11:43:12,970 combination with a more fine grained `package-data` configuration. 2025-09-14T11:43:12,970 You can read more about "package data files" on setuptools documentation page: 2025-09-14T11:43:12,970 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T11:43:12,970 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T11:43:12,970 even if it does not contain any `.py` files. 2025-09-14T11:43:12,971 On the other hand, currently there is no concept of package data 2025-09-14T11:43:12,971 directory, all directories are treated like packages. 2025-09-14T11:43:12,971 ******************************************************************************** 2025-09-14T11:43:12,971 !! 2025-09-14T11:43:12,971 check.warn(importable) 2025-09-14T11:43:12,971 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2025-09-14T11:43:12,971 !! 2025-09-14T11:43:12,971 ******************************************************************************** 2025-09-14T11:43:12,972 ############################ 2025-09-14T11:43:12,972 # Package would be ignored # 2025-09-14T11:43:12,972 ############################ 2025-09-14T11:43:12,972 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2025-09-14T11:43:12,972 but it is absent from setuptools' `packages` configuration. 2025-09-14T11:43:12,972 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T11:43:12,972 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2025-09-14T11:43:12,972 to the `packages` configuration field. 2025-09-14T11:43:12,973 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T11:43:12,973 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T11:43:12,973 instead of `find_packages(...)`/`find:`). 2025-09-14T11:43:12,973 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T11:43:12,973 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T11:43:12,973 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2025-09-14T11:43:12,973 already explicitly excluding 'uncalled4.vis.__pycache__' via 2025-09-14T11:43:12,973 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T11:43:12,974 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T11:43:12,974 combination with a more fine grained `package-data` configuration. 2025-09-14T11:43:12,974 You can read more about "package data files" on setuptools documentation page: 2025-09-14T11:43:12,974 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T11:43:12,974 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T11:43:12,974 even if it does not contain any `.py` files. 2025-09-14T11:43:12,974 On the other hand, currently there is no concept of package data 2025-09-14T11:43:12,975 directory, all directories are treated like packages. 2025-09-14T11:43:12,975 ******************************************************************************** 2025-09-14T11:43:12,975 !! 2025-09-14T11:43:12,975 check.warn(importable) 2025-09-14T11:43:12,975 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2025-09-14T11:43:12,975 !! 2025-09-14T11:43:12,975 ******************************************************************************** 2025-09-14T11:43:12,975 ############################ 2025-09-14T11:43:12,975 # Package would be ignored # 2025-09-14T11:43:12,976 ############################ 2025-09-14T11:43:12,976 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2025-09-14T11:43:12,976 but it is absent from setuptools' `packages` configuration. 2025-09-14T11:43:12,976 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-14T11:43:12,976 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2025-09-14T11:43:12,976 to the `packages` configuration field. 2025-09-14T11:43:12,976 Alternatively, you can also rely on setuptools' discovery methods 2025-09-14T11:43:12,976 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-14T11:43:12,976 instead of `find_packages(...)`/`find:`). 2025-09-14T11:43:12,977 You can read more about "package discovery" on setuptools documentation page: 2025-09-14T11:43:12,977 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-14T11:43:12,977 If you don't want 'uncalled4.vis.assets' to be distributed and are 2025-09-14T11:43:12,977 already explicitly excluding 'uncalled4.vis.assets' via 2025-09-14T11:43:12,977 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-14T11:43:12,977 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-14T11:43:12,977 combination with a more fine grained `package-data` configuration. 2025-09-14T11:43:12,977 You can read more about "package data files" on setuptools documentation page: 2025-09-14T11:43:12,978 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-14T11:43:12,978 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-14T11:43:12,978 even if it does not contain any `.py` files. 2025-09-14T11:43:12,978 On the other hand, currently there is no concept of package data 2025-09-14T11:43:12,978 directory, all directories are treated like packages. 2025-09-14T11:43:12,978 ******************************************************************************** 2025-09-14T11:43:12,978 !! 2025-09-14T11:43:12,979 check.warn(importable) 2025-09-14T11:43:12,979 creating build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,979 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 copying src/uncalled4/__pycache__/train.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/__pycache__ 2025-09-14T11:43:12,980 creating build/lib.linux-armv7l-cpython-313/uncalled4/models 2025-09-14T11:43:12,981 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-313/uncalled4/models 2025-09-14T11:43:12,981 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-313/uncalled4/models 2025-09-14T11:43:12,995 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer_sh3.npz -> build/lib.linux-armv7l-cpython-313/uncalled4/models 2025-09-14T11:43:13,016 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-313/uncalled4/models 2025-09-14T11:43:13,017 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-313/uncalled4/models 2025-09-14T11:43:13,017 copying src/uncalled4/models/rna004_130bps_9mer.npz -> build/lib.linux-armv7l-cpython-313/uncalled4/models 2025-09-14T11:43:13,024 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-313/uncalled4/models 2025-09-14T11:43:13,024 creating build/lib.linux-armv7l-cpython-313/uncalled4/models/tombo 2025-09-14T11:43:13,025 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-313/uncalled4/models/tombo 2025-09-14T11:43:13,025 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-313/uncalled4/models/tombo 2025-09-14T11:43:13,026 creating build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,026 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,027 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,027 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,028 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,028 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,029 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,029 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,030 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,031 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,031 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,032 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,032 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,033 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,033 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,034 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/__pycache__ 2025-09-14T11:43:13,034 creating build/lib.linux-armv7l-cpython-313/uncalled4/vis/assets 2025-09-14T11:43:13,035 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/assets 2025-09-14T11:43:13,035 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-313/uncalled4/vis/assets 2025-09-14T11:43:13,036 creating build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,036 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,036 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,037 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,037 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,038 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,038 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,039 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,039 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,040 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,040 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,041 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,041 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,042 copying src/uncalled4/stats/__pycache__/readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,043 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,043 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/stats/__pycache__ 2025-09-14T11:43:13,044 creating build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,044 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,044 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,045 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,045 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,046 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,047 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,047 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,048 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,048 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,049 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-313/uncalled4/io/__pycache__ 2025-09-14T11:43:13,051 running build_ext 2025-09-14T11:43:13,409 building '_uncalled4' extension 2025-09-14T11:43:13,426 creating build/temp.linux-armv7l-cpython-313/src/cpp 2025-09-14T11:43:13,428 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DPYBIND -I/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.13 -c src/cpp/config.cpp -o build/temp.linux-armv7l-cpython-313/src/cpp/config.o -std=c++11 -O3 -g 2025-09-14T11:43:19,192 In file included from src/cpp/dtw.hpp:7, 2025-09-14T11:43:19,193 from src/cpp/config.hpp:30, 2025-09-14T11:43:19,193 from src/cpp/config.cpp:1: 2025-09-14T11:43:19,193 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:19,193 src/cpp/intervals.hpp:110:20: required from here 2025-09-14T11:43:19,193 110 | if (starts_.size() != lengths_.size()) { 2025-09-14T11:43:19,193 | ^ 2025-09-14T11:43:19,193 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:19,193 192 | struct PyArray { 2025-09-14T11:43:19,193 | ^~~~~~~ 2025-09-14T11:43:19,367 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:19,368 src/cpp/read_buffer.hpp:99:38: required from here 2025-09-14T11:43:19,368 99 | PyArray moves_(moves_py); 2025-09-14T11:43:19,368 | ^ 2025-09-14T11:43:19,368 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:19,368 192 | struct PyArray { 2025-09-14T11:43:19,368 | ^~~~~~~ 2025-09-14T11:43:19,441 In file included from src/cpp/aln.hpp:11, 2025-09-14T11:43:19,441 from src/cpp/dtw.hpp:9: 2025-09-14T11:43:19,441 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2025-09-14T11:43:19,441 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:43:19,441 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2025-09-14T11:43:19,441 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-14T11:43:19,442 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:43:19,442 65 | while (i < events.size() && events[i].start < c.end) { 2025-09-14T11:43:19,464 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2025-09-14T11:43:19,464 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] 2025-09-14T11:43:19,464 147 | for (size_t i = prms.start; i < prms.end; i++) { 2025-09-14T11:43:19,464 | ~~^~~~~~~~~~ 2025-09-14T11:43:19,465 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2025-09-14T11:43:19,465 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] 2025-09-14T11:43:19,465 158 | normalize({0, events.size(), scale, shift}); 2025-09-14T11:43:19,466 | ~~~~~~~~~~~^~ 2025-09-14T11:43:19,504 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:19,505 src/cpp/event_detector.hpp:222:39: required from here 2025-09-14T11:43:19,505 222 | auto evts = PyArray(arr); 2025-09-14T11:43:19,505 | ^ 2025-09-14T11:43:19,505 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:19,505 192 | struct PyArray { 2025-09-14T11:43:19,505 | ^~~~~~~ 2025-09-14T11:43:19,599 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2025-09-14T11:43:19,599 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2025-09-14T11:43:19,599 188 | i64 ref; 2025-09-14T11:43:19,599 | ^~~ 2025-09-14T11:43:19,604 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2025-09-14T11:43:19,604 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2025-09-14T11:43:19,604 280 | int len,dist; 2025-09-14T11:43:19,605 | ^~~~ 2025-09-14T11:43:19,615 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:19,616 src/cpp/aln.hpp:385:23: required from here 2025-09-14T11:43:19,616 385 | if (cost[i] < best) { 2025-09-14T11:43:19,616 | ^ 2025-09-14T11:43:19,616 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:19,616 192 | struct PyArray { 2025-09-14T11:43:19,616 | ^~~~~~~ 2025-09-14T11:43:19,684 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:19,684 src/cpp/dtw.hpp:395:26: required from here 2025-09-14T11:43:19,684 395 | i32 orig = -ll_[0].ref; 2025-09-14T11:43:19,684 | ^ 2025-09-14T11:43:19,684 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:19,684 192 | struct PyArray { 2025-09-14T11:43:19,684 | ^~~~~~~ 2025-09-14T11:43:35,864 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DPYBIND -I/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.13 -c src/cpp/dtw.cpp -o build/temp.linux-armv7l-cpython-313/src/cpp/dtw.o -std=c++11 -O3 -g 2025-09-14T11:43:41,645 In file included from src/cpp/dtw.hpp:7, 2025-09-14T11:43:41,645 from src/cpp/dtw.cpp:1: 2025-09-14T11:43:41,645 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:41,645 src/cpp/intervals.hpp:110:20: required from here 2025-09-14T11:43:41,646 110 | if (starts_.size() != lengths_.size()) { 2025-09-14T11:43:41,646 | ^ 2025-09-14T11:43:41,646 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:41,646 192 | struct PyArray { 2025-09-14T11:43:41,646 | ^~~~~~~ 2025-09-14T11:43:41,819 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:41,820 src/cpp/read_buffer.hpp:99:38: required from here 2025-09-14T11:43:41,820 99 | PyArray moves_(moves_py); 2025-09-14T11:43:41,820 | ^ 2025-09-14T11:43:41,820 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:41,820 192 | struct PyArray { 2025-09-14T11:43:41,820 | ^~~~~~~ 2025-09-14T11:43:41,893 In file included from src/cpp/aln.hpp:11, 2025-09-14T11:43:41,893 from src/cpp/dtw.hpp:9: 2025-09-14T11:43:41,893 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2025-09-14T11:43:41,893 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:43:41,893 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2025-09-14T11:43:41,893 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-14T11:43:41,894 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:43:41,894 65 | while (i < events.size() && events[i].start < c.end) { 2025-09-14T11:43:41,915 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2025-09-14T11:43:41,916 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] 2025-09-14T11:43:41,916 147 | for (size_t i = prms.start; i < prms.end; i++) { 2025-09-14T11:43:41,916 | ~~^~~~~~~~~~ 2025-09-14T11:43:41,917 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2025-09-14T11:43:41,917 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] 2025-09-14T11:43:41,917 158 | normalize({0, events.size(), scale, shift}); 2025-09-14T11:43:41,917 | ~~~~~~~~~~~^~ 2025-09-14T11:43:41,956 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:41,957 src/cpp/event_detector.hpp:222:39: required from here 2025-09-14T11:43:41,957 222 | auto evts = PyArray(arr); 2025-09-14T11:43:41,957 | ^ 2025-09-14T11:43:41,957 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:41,957 192 | struct PyArray { 2025-09-14T11:43:41,957 | ^~~~~~~ 2025-09-14T11:43:42,051 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2025-09-14T11:43:42,051 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2025-09-14T11:43:42,051 188 | i64 ref; 2025-09-14T11:43:42,051 | ^~~ 2025-09-14T11:43:42,056 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2025-09-14T11:43:42,056 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2025-09-14T11:43:42,056 280 | int len,dist; 2025-09-14T11:43:42,057 | ^~~~ 2025-09-14T11:43:42,068 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:42,068 src/cpp/aln.hpp:385:23: required from here 2025-09-14T11:43:42,068 385 | if (cost[i] < best) { 2025-09-14T11:43:42,068 | ^ 2025-09-14T11:43:42,068 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:42,068 192 | struct PyArray { 2025-09-14T11:43:42,068 | ^~~~~~~ 2025-09-14T11:43:42,136 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:42,136 src/cpp/dtw.hpp:395:26: required from here 2025-09-14T11:43:42,136 395 | i32 orig = -ll_[0].ref; 2025-09-14T11:43:42,136 | ^ 2025-09-14T11:43:42,136 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:42,136 192 | struct PyArray { 2025-09-14T11:43:42,136 | ^~~~~~~ 2025-09-14T11:43:42,155 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2025-09-14T11:43:42,155 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2025-09-14T11:43:42,156 21 | size_t i = 0, j = 0, b = 0; 2025-09-14T11:43:42,156 | ^ 2025-09-14T11:43:42,160 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:43:42,161 src/cpp/dtw.cpp:64:30: required from here 2025-09-14T11:43:42,161 64 | PyArray refs(refs_py), qrys(qrys_py); 2025-09-14T11:43:42,161 | ^ 2025-09-14T11:43:42,161 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:43:42,161 192 | struct PyArray { 2025-09-14T11:43:42,161 | ^~~~~~~ 2025-09-14T11:43:42,167 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2025-09-14T11:43:42,167 src/cpp/dtw.cpp:99:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2025-09-14T11:43:42,167 99 | auto fill = backfill_na ? samps : Interval(); 2025-09-14T11:43:42,167 | ^~~~ 2025-09-14T11:44:51,613 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DPYBIND -I/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.13 -c src/cpp/event_detector.cpp -o build/temp.linux-armv7l-cpython-313/src/cpp/event_detector.o -std=c++11 -O3 -g 2025-09-14T11:44:57,426 In file included from src/cpp/intervals.hpp:11, 2025-09-14T11:44:57,427 from src/cpp/event_detector.hpp:13, 2025-09-14T11:44:57,427 from src/cpp/event_detector.cpp:15: 2025-09-14T11:44:57,427 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:44:57,427 src/cpp/intervals.hpp:110:20: required from here 2025-09-14T11:44:57,427 110 | if (starts_.size() != lengths_.size()) { 2025-09-14T11:44:57,427 | ^ 2025-09-14T11:44:57,427 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:44:57,427 192 | struct PyArray { 2025-09-14T11:44:57,428 | ^~~~~~~ 2025-09-14T11:44:57,448 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:44:57,448 src/cpp/read_buffer.hpp:99:38: required from here 2025-09-14T11:44:57,448 99 | PyArray moves_(moves_py); 2025-09-14T11:44:57,448 | ^ 2025-09-14T11:44:57,448 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:44:57,448 192 | struct PyArray { 2025-09-14T11:44:57,448 | ^~~~~~~ 2025-09-14T11:44:57,524 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2025-09-14T11:44:57,524 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:44:57,525 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2025-09-14T11:44:57,525 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-14T11:44:57,525 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:44:57,525 65 | while (i < events.size() && events[i].start < c.end) { 2025-09-14T11:44:57,550 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2025-09-14T11:44:57,551 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] 2025-09-14T11:44:57,551 147 | for (size_t i = prms.start; i < prms.end; i++) { 2025-09-14T11:44:57,551 | ~~^~~~~~~~~~ 2025-09-14T11:44:57,551 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2025-09-14T11:44:57,551 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] 2025-09-14T11:44:57,552 158 | normalize({0, events.size(), scale, shift}); 2025-09-14T11:44:57,552 | ~~~~~~~~~~~^~ 2025-09-14T11:44:57,590 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:44:57,591 src/cpp/event_detector.hpp:222:39: required from here 2025-09-14T11:44:57,591 222 | auto evts = PyArray(arr); 2025-09-14T11:44:57,591 | ^ 2025-09-14T11:44:57,591 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:44:57,591 192 | struct PyArray { 2025-09-14T11:44:57,591 | ^~~~~~~ 2025-09-14T11:44:57,646 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:44:57,646 src/cpp/event_detector.cpp:250:30: required from here 2025-09-14T11:44:57,646 250 | PyArray raw(raw_py); 2025-09-14T11:44:57,646 | ^ 2025-09-14T11:44:57,646 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:44:57,646 192 | struct PyArray { 2025-09-14T11:44:57,646 | ^~~~~~~ 2025-09-14T11:45:25,285 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DPYBIND -I/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.13 -c src/cpp/intervals.cpp -o build/temp.linux-armv7l-cpython-313/src/cpp/intervals.o -std=c++11 -O3 -g 2025-09-14T11:45:31,062 In file included from src/cpp/intervals.hpp:11, 2025-09-14T11:45:31,062 from src/cpp/intervals.cpp:2: 2025-09-14T11:45:31,062 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:45:31,063 src/cpp/intervals.hpp:110:20: required from here 2025-09-14T11:45:31,063 110 | if (starts_.size() != lengths_.size()) { 2025-09-14T11:45:31,063 | ^ 2025-09-14T11:45:31,063 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:45:31,063 192 | struct PyArray { 2025-09-14T11:45:31,063 | ^~~~~~~ 2025-09-14T11:45:32,866 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2025-09-14T11:45:32,866 src/cpp/intervals.hpp:467:31: required from ‘static void IntervalIndex::pybind(pybind11::module_&, const std::string&) [with T = int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:45:32,866 467 | .def("to_runlen", &IntervalIndex::to_runlen) 2025-09-14T11:45:32,866 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:45:32,866 src/cpp/intervals.cpp:7:31: required from here 2025-09-14T11:45:32,866 7 | IntervalIndex::pybind(m, "I32"); 2025-09-14T11:45:32,867 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:45:32,867 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] 2025-09-14T11:45:32,867 348 | while (gap >= MAX_LEN_I16) { 2025-09-14T11:45:32,867 | ~~~~^~~~~~~~~~~~~~ 2025-09-14T11:46:33,270 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DPYBIND -I/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.13 -c src/cpp/normalizer.cpp -o build/temp.linux-armv7l-cpython-313/src/cpp/normalizer.o -std=c++11 -O3 -g 2025-09-14T11:46:44,289 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DPYBIND -I/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.13 -c src/cpp/pore_model.cpp -o build/temp.linux-armv7l-cpython-313/src/cpp/pore_model.o -std=c++11 -O3 -g 2025-09-14T11:46:50,052 In file included from src/cpp/pore_model.hpp:36, 2025-09-14T11:46:50,053 from src/cpp/pore_model.cpp:1: 2025-09-14T11:46:50,053 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:46:50,053 src/cpp/intervals.hpp:110:20: required from here 2025-09-14T11:46:50,053 110 | if (starts_.size() != lengths_.size()) { 2025-09-14T11:46:50,053 | ^ 2025-09-14T11:46:50,053 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:46:50,053 192 | struct PyArray { 2025-09-14T11:46:50,053 | ^~~~~~~ 2025-09-14T11:47:27,937 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DPYBIND -I/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.13 -c src/cpp/pybinder.cpp -o build/temp.linux-armv7l-cpython-313/src/cpp/pybinder.o -std=c++11 -O3 -g 2025-09-14T11:47:33,763 In file included from src/cpp/read_buffer.hpp:30, 2025-09-14T11:47:33,764 from src/cpp/pybinder.cpp:5: 2025-09-14T11:47:33,764 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:47:33,764 src/cpp/read_buffer.hpp:99:38: required from here 2025-09-14T11:47:33,764 99 | PyArray moves_(moves_py); 2025-09-14T11:47:33,764 | ^ 2025-09-14T11:47:33,764 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:47:33,764 192 | struct PyArray { 2025-09-14T11:47:33,764 | ^~~~~~~ 2025-09-14T11:47:33,815 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:47:33,815 src/cpp/intervals.hpp:110:20: required from here 2025-09-14T11:47:33,815 110 | if (starts_.size() != lengths_.size()) { 2025-09-14T11:47:33,815 | ^ 2025-09-14T11:47:33,815 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:47:33,815 192 | struct PyArray { 2025-09-14T11:47:33,816 | ^~~~~~~ 2025-09-14T11:47:33,893 In file included from src/cpp/signal_processor.hpp:7, 2025-09-14T11:47:33,893 from src/cpp/pybinder.cpp:6: 2025-09-14T11:47:33,893 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2025-09-14T11:47:33,893 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:47:33,893 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2025-09-14T11:47:33,894 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-14T11:47:33,894 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:47:33,894 65 | while (i < events.size() && events[i].start < c.end) { 2025-09-14T11:47:33,919 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2025-09-14T11:47:33,919 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] 2025-09-14T11:47:33,919 147 | for (size_t i = prms.start; i < prms.end; i++) { 2025-09-14T11:47:33,919 | ~~^~~~~~~~~~ 2025-09-14T11:47:33,920 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2025-09-14T11:47:33,920 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] 2025-09-14T11:47:33,920 158 | normalize({0, events.size(), scale, shift}); 2025-09-14T11:47:33,920 | ~~~~~~~~~~~^~ 2025-09-14T11:47:33,959 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:47:33,959 src/cpp/event_detector.hpp:222:39: required from here 2025-09-14T11:47:33,959 222 | auto evts = PyArray(arr); 2025-09-14T11:47:33,959 | ^ 2025-09-14T11:47:33,959 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:47:33,960 192 | struct PyArray { 2025-09-14T11:47:33,960 | ^~~~~~~ 2025-09-14T11:47:34,200 In file included from src/cpp/dtw.hpp:9, 2025-09-14T11:47:34,200 from src/cpp/pybinder.cpp:8: 2025-09-14T11:47:34,200 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2025-09-14T11:47:34,200 src/cpp/aln.hpp:188:13: warning: unused variable ‘ref’ [-Wunused-variable] 2025-09-14T11:47:34,200 188 | i64 ref; 2025-09-14T11:47:34,200 | ^~~ 2025-09-14T11:47:34,204 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2025-09-14T11:47:34,204 src/cpp/aln.hpp:280:21: warning: unused variable ‘dist’ [-Wunused-variable] 2025-09-14T11:47:34,205 280 | int len,dist; 2025-09-14T11:47:34,205 | ^~~~ 2025-09-14T11:47:34,215 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:47:34,215 src/cpp/aln.hpp:385:23: required from here 2025-09-14T11:47:34,215 385 | if (cost[i] < best) { 2025-09-14T11:47:34,215 | ^ 2025-09-14T11:47:34,216 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:47:34,216 192 | struct PyArray { 2025-09-14T11:47:34,216 | ^~~~~~~ 2025-09-14T11:47:34,282 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:47:34,283 src/cpp/dtw.hpp:395:26: required from here 2025-09-14T11:47:34,283 395 | i32 orig = -ll_[0].ref; 2025-09-14T11:47:34,283 | ^ 2025-09-14T11:47:34,283 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:47:34,283 192 | struct PyArray { 2025-09-14T11:47:34,283 | ^~~~~~~ 2025-09-14T11:47:34,319 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:47:34,319 src/cpp/eventalign.hpp:110:31: required from here 2025-09-14T11:47:34,320 110 | for (size_t i = 0; i < ref.size(); i++) { 2025-09-14T11:47:34,320 | ^ 2025-09-14T11:47:34,320 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:47:34,320 192 | struct PyArray { 2025-09-14T11:47:34,320 | ^~~~~~~ 2025-09-14T11:47:37,641 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:47:37,641 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const std::string&, pybind11::array_t, bool, pybind11::array_t, pybind11::array_t, pybind11::array_t, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string; typename ModelType::kmer_t = short unsigned int]’ 2025-09-14T11:47:37,641 101 | auto kmers = PyArray(kmer_np); 2025-09-14T11:47:37,641 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:37,641 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]’ 2025-09-14T11:47:37,642 31 | auto fn = write_eventalign; 2025-09-14T11:47:37,642 | ^~ 2025-09-14T11:47:37,642 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:47:37,642 66 | pybind_model(m, "U16"); 2025-09-14T11:47:37,642 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:37,642 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:47:37,642 192 | struct PyArray { 2025-09-14T11:47:37,642 | ^~~~~~~ 2025-09-14T11:47:37,668 In file included from src/cpp/pybinder.cpp:10: 2025-09-14T11:47:37,668 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]’: 2025-09-14T11:47:37,668 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]’ 2025-09-14T11:47:37,668 34 | auto fn_new = write_eventalign_new; 2025-09-14T11:47:37,668 | ^~~~~~ 2025-09-14T11:47:37,668 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:47:37,668 66 | pybind_model(m, "U16"); 2025-09-14T11:47:37,668 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:37,669 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:47:37,669 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2025-09-14T11:47:37,669 | ~~^~~~~~~~~~~ 2025-09-14T11:47:37,811 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2025-09-14T11:47:37,811 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const std::string&, pybind11::array_t, bool, pybind11::array_t, pybind11::array_t, pybind11::array_t, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string; typename ModelType::kmer_t = unsigned int]’ 2025-09-14T11:47:37,811 101 | auto kmers = PyArray(kmer_np); 2025-09-14T11:47:37,811 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:37,811 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]’ 2025-09-14T11:47:37,811 31 | auto fn = write_eventalign; 2025-09-14T11:47:37,811 | ^~ 2025-09-14T11:47:37,811 src/cpp/pybinder.cpp:67:22: required from here 2025-09-14T11:47:37,812 67 | pybind_model(m, "U32"); 2025-09-14T11:47:37,812 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:37,812 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2025-09-14T11:47:37,812 192 | struct PyArray { 2025-09-14T11:47:37,812 | ^~~~~~~ 2025-09-14T11:47:37,836 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]’: 2025-09-14T11:47:37,836 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]’ 2025-09-14T11:47:37,836 34 | auto fn_new = write_eventalign_new; 2025-09-14T11:47:37,836 | ^~~~~~ 2025-09-14T11:47:37,836 src/cpp/pybinder.cpp:67:22: required from here 2025-09-14T11:47:37,836 67 | pybind_model(m, "U32"); 2025-09-14T11:47:37,836 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:37,836 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-14T11:47:37,836 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2025-09-14T11:47:37,837 | ~~^~~~~~~~~~~ 2025-09-14T11:47:42,036 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2025-09-14T11:47:42,036 src/cpp/dtw.hpp:736:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:42,036 711 | #define PY_BANDED_DTW_METH(P) c.def(#P, &BandedDTW::P); 2025-09-14T11:47:42,037 | ^ 2025-09-14T11:47:42,037 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]’ 2025-09-14T11:47:42,037 23 | BandedDTW::pybind_defs(m, suffix); 2025-09-14T11:47:42,037 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:47:42,037 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:47:42,037 66 | pybind_model(m, "U16"); 2025-09-14T11:47:42,037 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:42,037 src/cpp/dtw.hpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-14T11:47:42,037 646 | if (q0 >= qry_size()) { 2025-09-14T11:47:42,038 | ~~~^~~~~~~~~~~~~ 2025-09-14T11:47:42,038 src/cpp/dtw.hpp:653:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-14T11:47:42,038 653 | if (r1 > ref_size()) { 2025-09-14T11:47:42,038 | ~~~^~~~~~~~~~~~ 2025-09-14T11:47:42,473 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2025-09-14T11:47:42,473 src/cpp/dtw.hpp:736:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:42,473 711 | #define PY_BANDED_DTW_METH(P) c.def(#P, &BandedDTW::P); 2025-09-14T11:47:42,473 | ^ 2025-09-14T11:47:42,473 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]’ 2025-09-14T11:47:42,474 23 | BandedDTW::pybind_defs(m, suffix); 2025-09-14T11:47:42,474 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:47:42,474 src/cpp/pybinder.cpp:67:22: required from here 2025-09-14T11:47:42,474 67 | pybind_model(m, "U32"); 2025-09-14T11:47:42,474 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:42,474 src/cpp/dtw.hpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-14T11:47:42,474 646 | if (q0 >= qry_size()) { 2025-09-14T11:47:42,474 | ~~~^~~~~~~~~~~~~ 2025-09-14T11:47:42,474 src/cpp/dtw.hpp:653:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-14T11:47:42,475 653 | if (r1 > ref_size()) { 2025-09-14T11:47:42,475 | ~~~^~~~~~~~~~~~ 2025-09-14T11:47:52,682 In file included from src/cpp/seq.hpp:32, 2025-09-14T11:47:52,682 from src/cpp/pybinder.cpp:7: 2025-09-14T11:47:52,682 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]’: 2025-09-14T11:47:52,682 src/cpp/pore_model.hpp:505:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:52,683 505 | return str_to_kmers(seq.begin()+KMER_LEN, dest, n, init_kmer, comp); 2025-09-14T11:47:52,683 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:52,683 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:52,683 489 | str_to_kmers(seq, std::begin(ret), rev, comp); 2025-09-14T11:47:52,683 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:52,683 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:52,683 681 | static_cast (PoreModel::*) (const std::string &, bool, bool) const>(&Class::str_to_kmers), py::arg("seq"), py::arg("rev")=false, py::arg("comp")=false); 2025-09-14T11:47:52,683 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:52,683 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]’ 2025-09-14T11:47:52,684 21 | Model::pybind(m, suffix); 2025-09-14T11:47:52,684 | ~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:47:52,684 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:47:52,684 66 | pybind_model(m, "U16"); 2025-09-14T11:47:52,684 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:52,684 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-14T11:47:52,684 516 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2025-09-14T11:47:52,684 | ~~~~~~~~~~^ 2025-09-14T11:47:52,684 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]’: 2025-09-14T11:47:52,685 src/cpp/pore_model.hpp:507:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:52,685 507 | return str_to_kmers(seq.rbegin()+KMER_LEN, dest, n, init_kmer, comp); 2025-09-14T11:47:52,685 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:52,685 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:52,685 489 | str_to_kmers(seq, std::begin(ret), rev, comp); 2025-09-14T11:47:52,685 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:52,685 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:52,685 681 | static_cast (PoreModel::*) (const std::string &, bool, bool) const>(&Class::str_to_kmers), py::arg("seq"), py::arg("rev")=false, py::arg("comp")=false); 2025-09-14T11:47:52,685 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:52,685 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]’ 2025-09-14T11:47:52,686 21 | Model::pybind(m, suffix); 2025-09-14T11:47:52,686 | ~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:47:52,686 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:47:52,686 66 | pybind_model(m, "U16"); 2025-09-14T11:47:52,686 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:52,686 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-14T11:47:52,686 516 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2025-09-14T11:47:52,686 | ~~~~~~~~~~^ 2025-09-14T11:47:54,602 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]’: 2025-09-14T11:47:54,602 src/cpp/pore_model.hpp:505:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:54,602 505 | return str_to_kmers(seq.begin()+KMER_LEN, dest, n, init_kmer, comp); 2025-09-14T11:47:54,602 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:54,602 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:54,603 489 | str_to_kmers(seq, std::begin(ret), rev, comp); 2025-09-14T11:47:54,603 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:54,603 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:54,603 681 | static_cast (PoreModel::*) (const std::string &, bool, bool) const>(&Class::str_to_kmers), py::arg("seq"), py::arg("rev")=false, py::arg("comp")=false); 2025-09-14T11:47:54,603 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:54,603 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]’ 2025-09-14T11:47:54,603 21 | Model::pybind(m, suffix); 2025-09-14T11:47:54,603 | ~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:47:54,603 src/cpp/pybinder.cpp:67:22: required from here 2025-09-14T11:47:54,604 67 | pybind_model(m, "U32"); 2025-09-14T11:47:54,604 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:54,604 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-14T11:47:54,604 516 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2025-09-14T11:47:54,604 | ~~~~~~~~~~^ 2025-09-14T11:47:54,604 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]’: 2025-09-14T11:47:54,604 src/cpp/pore_model.hpp:507:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:54,604 507 | return str_to_kmers(seq.rbegin()+KMER_LEN, dest, n, init_kmer, comp); 2025-09-14T11:47:54,604 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:54,605 src/cpp/pore_model.hpp:489:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:54,605 489 | str_to_kmers(seq, std::begin(ret), rev, comp); 2025-09-14T11:47:54,605 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:54,605 src/cpp/pore_model.hpp:681:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:54,605 681 | static_cast (PoreModel::*) (const std::string &, bool, bool) const>(&Class::str_to_kmers), py::arg("seq"), py::arg("rev")=false, py::arg("comp")=false); 2025-09-14T11:47:54,605 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:54,605 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]’ 2025-09-14T11:47:54,605 21 | Model::pybind(m, suffix); 2025-09-14T11:47:54,605 | ~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:47:54,606 src/cpp/pybinder.cpp:67:22: required from here 2025-09-14T11:47:54,606 67 | pybind_model(m, "U32"); 2025-09-14T11:47:54,606 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:54,606 src/cpp/pore_model.hpp:516:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-14T11:47:54,606 516 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2025-09-14T11:47:54,606 | ~~~~~~~~~~^ 2025-09-14T11:47:59,732 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]’: 2025-09-14T11:47:59,732 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2025-09-14T11:47:59,733 340 | init_current(current_mean, current_stdv, _, _, preprocess); 2025-09-14T11:47:59,733 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:59,733 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:77:12: 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]’ 2025-09-14T11:47:59,733 77 | return new Class(std::forward(args)...); 2025-09-14T11:47:59,733 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:59,733 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:301:70: 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}]’ 2025-09-14T11:47:59,733 301 | v_h.value_ptr() = construct_or_initialize>(std::forward(args)...); 2025-09-14T11:47:59,733 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:59,733 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/pybind11.h:2199:21: 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 = {}]’ 2025-09-14T11:47:59,734 2199 | init.execute(*this, extra...); 2025-09-14T11:47:59,734 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-14T11:47:59,734 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:47:59,734 655 | c.def(pybind11::init, py::array_t, bool>()); 2025-09-14T11:47:59,734 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:47:59,734 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]’ 2025-09-14T11:47:59,734 21 | Model::pybind(m, suffix); 2025-09-14T11:47:59,734 | ~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:47:59,734 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:47:59,735 66 | pybind_model(m, "U16"); 2025-09-14T11:47:59,735 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:47:59,735 src/cpp/pore_model.hpp:355:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2025-09-14T11:47:59,735 355 | auto get_kmer = [&](size_t i) {return i;}; 2025-09-14T11:47:59,735 | ^~~~~~~~ 2025-09-14T11:48:00,155 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2025-09-14T11:48:00,155 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]’ 2025-09-14T11:48:00,155 356 | fill_mat(); 2025-09-14T11:48:00,155 | ^~~~~~~~ 2025-09-14T11:48:00,155 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:77:12: 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]’ 2025-09-14T11:48:00,156 77 | return new Class(std::forward(args)...); 2025-09-14T11:48:00,156 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,156 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:301:70: 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&}]’ 2025-09-14T11:48:00,156 301 | v_h.value_ptr() = construct_or_initialize>(std::forward(args)...); 2025-09-14T11:48:00,156 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,156 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/pybind11.h:2199:21: 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 = {}]’ 2025-09-14T11:48:00,156 2199 | init.execute(*this, extra...); 2025-09-14T11:48:00,156 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,156 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:48:00,156 716 | c.def(pybind11::init&, 2025-09-14T11:48:00,157 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,157 718 | const ProcessedRead&, 2025-09-14T11:48:00,157 | ~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,157 719 | size_t, size_t, 2025-09-14T11:48:00,157 | ~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,157 720 | const std::vector&, 2025-09-14T11:48:00,157 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,157 721 | const ModelType&, 2025-09-14T11:48:00,158 | ~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,158 722 | const PyArray&>()); 2025-09-14T11:48:00,158 | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,158 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]’ 2025-09-14T11:48:00,158 23 | BandedDTW::pybind_defs(m, suffix); 2025-09-14T11:48:00,158 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:48:00,158 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:48:00,158 66 | pybind_model(m, "U16"); 2025-09-14T11:48:00,158 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:48:00,158 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] 2025-09-14T11:48:00,158 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2025-09-14T11:48:00,159 | ~~^~~~~~~~~~~~ 2025-09-14T11:48:00,159 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2025-09-14T11:48:00,159 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]’ 2025-09-14T11:48:00,159 357 | traceback(); 2025-09-14T11:48:00,159 | ^~~~~~~~~ 2025-09-14T11:48:00,159 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:77:12: 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]’ 2025-09-14T11:48:00,159 77 | return new Class(std::forward(args)...); 2025-09-14T11:48:00,159 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,160 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:301:70: 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&}]’ 2025-09-14T11:48:00,160 301 | v_h.value_ptr() = construct_or_initialize>(std::forward(args)...); 2025-09-14T11:48:00,160 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,160 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/pybind11.h:2199:21: 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 = {}]’ 2025-09-14T11:48:00,160 2199 | init.execute(*this, extra...); 2025-09-14T11:48:00,160 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,160 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:48:00,160 716 | c.def(pybind11::init&, 2025-09-14T11:48:00,161 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,161 718 | const ProcessedRead&, 2025-09-14T11:48:00,161 | ~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,161 719 | size_t, size_t, 2025-09-14T11:48:00,161 | ~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,161 720 | const std::vector&, 2025-09-14T11:48:00,161 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,161 721 | const ModelType&, 2025-09-14T11:48:00,161 | ~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,161 722 | const PyArray&>()); 2025-09-14T11:48:00,162 | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:00,162 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]’ 2025-09-14T11:48:00,162 23 | BandedDTW::pybind_defs(m, suffix); 2025-09-14T11:48:00,162 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:48:00,162 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:48:00,162 66 | pybind_model(m, "U16"); 2025-09-14T11:48:00,162 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:48:00,162 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] 2025-09-14T11:48:00,162 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2025-09-14T11:48:00,163 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2025-09-14T11:48:03,571 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]’: 2025-09-14T11:48:03,571 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2025-09-14T11:48:03,571 340 | init_current(current_mean, current_stdv, _, _, preprocess); 2025-09-14T11:48:03,571 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,572 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:77:12: 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]’ 2025-09-14T11:48:03,572 77 | return new Class(std::forward(args)...); 2025-09-14T11:48:03,572 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,572 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:301:70: 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}]’ 2025-09-14T11:48:03,572 301 | v_h.value_ptr() = construct_or_initialize>(std::forward(args)...); 2025-09-14T11:48:03,572 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,572 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/pybind11.h:2199:21: 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 = {}]’ 2025-09-14T11:48:03,573 2199 | init.execute(*this, extra...); 2025-09-14T11:48:03,573 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,573 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:48:03,573 655 | c.def(pybind11::init, py::array_t, bool>()); 2025-09-14T11:48:03,573 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,573 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]’ 2025-09-14T11:48:03,573 21 | Model::pybind(m, suffix); 2025-09-14T11:48:03,573 | ~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:48:03,573 src/cpp/pybinder.cpp:67:22: required from here 2025-09-14T11:48:03,573 67 | pybind_model(m, "U32"); 2025-09-14T11:48:03,574 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:48:03,574 src/cpp/pore_model.hpp:355:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2025-09-14T11:48:03,574 355 | auto get_kmer = [&](size_t i) {return i;}; 2025-09-14T11:48:03,574 | ^~~~~~~~ 2025-09-14T11:48:03,761 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2025-09-14T11:48:03,761 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]’ 2025-09-14T11:48:03,761 356 | fill_mat(); 2025-09-14T11:48:03,761 | ^~~~~~~~ 2025-09-14T11:48:03,761 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:77:12: 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]’ 2025-09-14T11:48:03,762 77 | return new Class(std::forward(args)...); 2025-09-14T11:48:03,762 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,762 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:301:70: 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&}]’ 2025-09-14T11:48:03,762 301 | v_h.value_ptr() = construct_or_initialize>(std::forward(args)...); 2025-09-14T11:48:03,762 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,762 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/pybind11.h:2199:21: 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 = {}]’ 2025-09-14T11:48:03,762 2199 | init.execute(*this, extra...); 2025-09-14T11:48:03,762 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,762 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:48:03,763 716 | c.def(pybind11::init&, 2025-09-14T11:48:03,763 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,763 718 | const ProcessedRead&, 2025-09-14T11:48:03,763 | ~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,763 719 | size_t, size_t, 2025-09-14T11:48:03,763 | ~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,763 720 | const std::vector&, 2025-09-14T11:48:03,763 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,763 721 | const ModelType&, 2025-09-14T11:48:03,764 | ~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,764 722 | const PyArray&>()); 2025-09-14T11:48:03,764 | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,764 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]’ 2025-09-14T11:48:03,764 23 | BandedDTW::pybind_defs(m, suffix); 2025-09-14T11:48:03,764 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:48:03,764 src/cpp/pybinder.cpp:67:22: required from here 2025-09-14T11:48:03,764 67 | pybind_model(m, "U32"); 2025-09-14T11:48:03,764 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:48:03,765 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] 2025-09-14T11:48:03,765 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2025-09-14T11:48:03,765 | ~~^~~~~~~~~~~~ 2025-09-14T11:48:03,765 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2025-09-14T11:48:03,765 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]’ 2025-09-14T11:48:03,765 357 | traceback(); 2025-09-14T11:48:03,765 | ^~~~~~~~~ 2025-09-14T11:48:03,765 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:77:12: 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]’ 2025-09-14T11:48:03,765 77 | return new Class(std::forward(args)...); 2025-09-14T11:48:03,766 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,766 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:301:70: 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&}]’ 2025-09-14T11:48:03,766 301 | v_h.value_ptr() = construct_or_initialize>(std::forward(args)...); 2025-09-14T11:48:03,766 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,766 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/pybind11.h:2199:21: 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 = {}]’ 2025-09-14T11:48:03,766 2199 | init.execute(*this, extra...); 2025-09-14T11:48:03,766 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,766 src/cpp/dtw.hpp:716:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:48:03,766 716 | c.def(pybind11::init&, 2025-09-14T11:48:03,767 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,767 718 | const ProcessedRead&, 2025-09-14T11:48:03,767 | ~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,767 719 | size_t, size_t, 2025-09-14T11:48:03,767 | ~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,767 720 | const std::vector&, 2025-09-14T11:48:03,767 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,767 721 | const ModelType&, 2025-09-14T11:48:03,767 | ~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,768 722 | const PyArray&>()); 2025-09-14T11:48:03,768 | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:03,768 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]’ 2025-09-14T11:48:03,768 23 | BandedDTW::pybind_defs(m, suffix); 2025-09-14T11:48:03,768 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:48:03,768 src/cpp/pybinder.cpp:67:22: required from here 2025-09-14T11:48:03,768 67 | pybind_model(m, "U32"); 2025-09-14T11:48:03,768 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:48:03,768 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] 2025-09-14T11:48:03,768 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2025-09-14T11:48:03,769 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2025-09-14T11:48:04,989 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2025-09-14T11:48:04,990 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]’ 2025-09-14T11:48:04,990 378 | PRMS.pa_mean = current.mean.mean(); 2025-09-14T11:48:04,990 | ~~~~~~~~~~~~~~~~~^~ 2025-09-14T11:48:04,990 src/cpp/pore_model.hpp:340:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2025-09-14T11:48:04,990 340 | init_current(current_mean, current_stdv, _, _, preprocess); 2025-09-14T11:48:04,990 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:04,990 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:77:12: 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]’ 2025-09-14T11:48:04,991 77 | return new Class(std::forward(args)...); 2025-09-14T11:48:04,991 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:04,991 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/detail/init.h:301:70: 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}]’ 2025-09-14T11:48:04,991 301 | v_h.value_ptr() = construct_or_initialize>(std::forward(args)...); 2025-09-14T11:48:04,991 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:04,991 /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/.eggs/pybind11-3.0.1-py3.13.egg/pybind11/include/pybind11/pybind11.h:2199:21: 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 = {}]’ 2025-09-14T11:48:04,992 2199 | init.execute(*this, extra...); 2025-09-14T11:48:04,992 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-14T11:48:04,992 src/cpp/pore_model.hpp:655:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2025-09-14T11:48:04,992 655 | c.def(pybind11::init, py::array_t, bool>()); 2025-09-14T11:48:04,992 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-14T11:48:04,992 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]’ 2025-09-14T11:48:04,993 21 | Model::pybind(m, suffix); 2025-09-14T11:48:04,993 | ~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-14T11:48:04,993 src/cpp/pybinder.cpp:66:22: required from here 2025-09-14T11:48:04,993 66 | pybind_model(m, "U16"); 2025-09-14T11:48:04,993 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-14T11:48:04,993 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2025-09-14T11:48:04,993 144 | auto sum = super::sum(); 2025-09-14T11:48:04,994 | ^~~ 2025-09-14T11:48:04,994 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2025-09-14T11:48:04,994 145 | auto len = super::size(); 2025-09-14T11:48:04,994 | ^~~ 2025-09-14T11:48:38,527 virtual memory exhausted: Cannot allocate memory 2025-09-14T11:48:38,636 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-14T11:48:38,782 ERROR: python setup.py bdist_wheel exited with 1 2025-09-14T11:48:38,794 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-14T11:48:38,794 exec(compile('"'"''"'"''"'"' 2025-09-14T11:48:38,794 # This is -- a caller that pip uses to run setup.py 2025-09-14T11:48:38,794 # 2025-09-14T11:48:38,794 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-14T11:48:38,794 # import from `distutils.core` to work with newer packaging standards. 2025-09-14T11:48:38,794 # - It provides a clear error message when setuptools is not installed. 2025-09-14T11:48:38,794 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-14T11:48:38,794 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-14T11:48:38,794 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-14T11:48:38,794 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-14T11:48:38,794 import os, sys, tokenize, traceback 2025-09-14T11:48:38,794 2025-09-14T11:48:38,794 try: 2025-09-14T11:48:38,794 import setuptools 2025-09-14T11:48:38,794 except ImportError: 2025-09-14T11:48:38,794 print( 2025-09-14T11:48:38,794 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-14T11:48:38,794 "the build environment with exception:", 2025-09-14T11:48:38,794 file=sys.stderr, 2025-09-14T11:48:38,794 ) 2025-09-14T11:48:38,794 traceback.print_exc() 2025-09-14T11:48:38,794 sys.exit(1) 2025-09-14T11:48:38,794 2025-09-14T11:48:38,794 __file__ = %r 2025-09-14T11:48:38,794 sys.argv[0] = __file__ 2025-09-14T11:48:38,794 2025-09-14T11:48:38,794 if os.path.exists(__file__): 2025-09-14T11:48:38,794 filename = __file__ 2025-09-14T11:48:38,794 with tokenize.open(__file__) as f: 2025-09-14T11:48:38,794 setup_py_code = f.read() 2025-09-14T11:48:38,794 else: 2025-09-14T11:48:38,794 filename = "" 2025-09-14T11:48:38,794 setup_py_code = "from setuptools import setup; setup()" 2025-09-14T11:48:38,794 2025-09-14T11:48:38,794 exec(compile(setup_py_code, filename, "exec")) 2025-09-14T11:48:38,794 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-_2gmue6v[/] 2025-09-14T11:48:38,794 [bold magenta]cwd[/]: /tmp/pip-wheel-xrmh8qzq/uncalled4_6c7c4b6232a441db9efcf7802c69ad1a/ 2025-09-14T11:48:38,794 Building wheel for uncalled4 (setup.py): finished with status 'error' 2025-09-14T11:48:38,795 ERROR: Failed building wheel for uncalled4 2025-09-14T11:48:38,795 Running setup.py clean for uncalled4 2025-09-14T11:48:38,796 Running command python setup.py clean 2025-09-14T11:48:39,725 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-14T11:48:39,725 !! 2025-09-14T11:48:39,726 ******************************************************************************** 2025-09-14T11:48:39,726 Requirements should be satisfied by a PEP 517 installer. 2025-09-14T11:48:39,726 If you are using pip, you can try `pip install --use-pep517`. 2025-09-14T11:48:39,726 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-14T11:48:39,726 or your builds will no longer be supported. 2025-09-14T11:48:39,726 ******************************************************************************** 2025-09-14T11:48:39,726 !! 2025-09-14T11:48:39,726 dist.fetch_build_eggs(dist.setup_requires) 2025-09-14T11:48:40,235 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'build_backend' 2025-09-14T11:48:40,235 warnings.warn(msg) 2025-09-14T11:48:40,508 running clean 2025-09-14T11:48:40,655 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-14T11:48:40,665 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-14T11:48:40,673 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-14T11:48:40,673 'build/scripts-3.13' does not exist -- can't clean it 2025-09-14T11:48:40,673 removing 'build' 2025-09-14T11:48:40,788 Failed to build uncalled4 2025-09-14T11:48:40,789 ERROR: Failed to build one or more wheels 2025-09-14T11:48:40,790 Exception information: 2025-09-14T11:48:40,790 Traceback (most recent call last): 2025-09-14T11:48:40,790 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-14T11:48:40,790 status = _inner_run() 2025-09-14T11:48:40,790 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-14T11:48:40,790 return self.run(options, args) 2025-09-14T11:48:40,790 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-14T11:48:40,790 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-14T11:48:40,790 return func(self, options, args) 2025-09-14T11:48:40,790 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-14T11:48:40,790 raise CommandError("Failed to build one or more wheels") 2025-09-14T11:48:40,790 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-14T11:48:40,795 Removed build tracker: '/tmp/pip-build-tracker-wmy651m9'