2024-03-05T18:19:41,676 Created temporary directory: /tmp/pip-build-tracker-f9upf843 2024-03-05T18:19:41,678 Initialized build tracking at /tmp/pip-build-tracker-f9upf843 2024-03-05T18:19:41,678 Created build tracker: /tmp/pip-build-tracker-f9upf843 2024-03-05T18:19:41,678 Entered build tracker: /tmp/pip-build-tracker-f9upf843 2024-03-05T18:19:41,679 Created temporary directory: /tmp/pip-wheel-j_89egjv 2024-03-05T18:19:41,683 Created temporary directory: /tmp/pip-ephem-wheel-cache-7csj92_0 2024-03-05T18:19:41,707 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-05T18:19:41,711 2 location(s) to search for versions of uncalled4: 2024-03-05T18:19:41,711 * https://pypi.org/simple/uncalled4/ 2024-03-05T18:19:41,711 * https://www.piwheels.org/simple/uncalled4/ 2024-03-05T18:19:41,711 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2024-03-05T18:19:41,712 Getting page https://pypi.org/simple/uncalled4/ 2024-03-05T18:19:41,713 Found index url https://pypi.org/simple/ 2024-03-05T18:19:41,767 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2024-03-05T18:19:41,768 Found link https://files.pythonhosted.org/packages/84/34/b2d0e57215e66cb04e9185ad6f858f3ded32b197dee61328b96d3dddd47a/uncalled4-3.5.1.tar.gz (from https://pypi.org/simple/uncalled4/) (requires-python:>=3.8), version: 3.5.1 2024-03-05T18:19:41,769 Found link https://files.pythonhosted.org/packages/bc/fd/a714f3b65dee9941ca73910515fd77bda3b6813c5832df5d4392221ad64b/uncalled4-4.0.0.tar.gz (from https://pypi.org/simple/uncalled4/) (requires-python:>=3.8), version: 4.0.0 2024-03-05T18:19:41,769 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2024-03-05T18:19:41,770 Getting page https://www.piwheels.org/simple/uncalled4/ 2024-03-05T18:19:41,771 Found index url https://www.piwheels.org/simple/ 2024-03-05T18:19:42,248 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2024-03-05T18:19:42,248 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2024-03-05T18:19:42,249 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2024-03-05T18:19:42,267 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2024-03-05T18:19:42,284 Collecting uncalled4==4.0.0 2024-03-05T18:19:42,287 Created temporary directory: /tmp/pip-unpack-67zepn52 2024-03-05T18:19:42,333 Downloading uncalled4-4.0.0.tar.gz (19.2 MB) 2024-03-05T18:19:49,865 Added uncalled4==4.0.0 from https://files.pythonhosted.org/packages/bc/fd/a714f3b65dee9941ca73910515fd77bda3b6813c5832df5d4392221ad64b/uncalled4-4.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-f9upf843' 2024-03-05T18:19:49,867 Running setup.py (path:/tmp/pip-wheel-j_89egjv/uncalled4_c1a18e3e383c4f32879ca8edd0d58ddc/setup.py) egg_info for package uncalled4 2024-03-05T18:19:49,868 Created temporary directory: /tmp/pip-pip-egg-info-9bi72nwq 2024-03-05T18:19:49,868 Preparing metadata (setup.py): started 2024-03-05T18:19:49,869 Running command python setup.py egg_info 2024-03-05T18:19:50,795 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-05T18:19:50,796 !! 2024-03-05T18:19:50,796 ******************************************************************************** 2024-03-05T18:19:50,796 Requirements should be satisfied by a PEP 517 installer. 2024-03-05T18:19:50,796 If you are using pip, you can try `pip install --use-pep517`. 2024-03-05T18:19:50,796 ******************************************************************************** 2024-03-05T18:19:50,797 !! 2024-03-05T18:19:50,797 dist.fetch_build_eggs(dist.setup_requires) 2024-03-05T18:19:50,871 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-05T18:19:50,871 warnings.warn(msg) 2024-03-05T18:19:51,103 running egg_info 2024-03-05T18:19:51,108 creating /tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info 2024-03-05T18:19:51,184 writing /tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info/PKG-INFO 2024-03-05T18:19:51,204 writing dependency_links to /tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info/dependency_links.txt 2024-03-05T18:19:51,213 writing entry points to /tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info/entry_points.txt 2024-03-05T18:19:51,220 writing requirements to /tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info/requires.txt 2024-03-05T18:19:51,226 writing top-level names to /tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info/top_level.txt 2024-03-05T18:19:51,234 writing manifest file '/tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info/SOURCES.txt' 2024-03-05T18:19:51,530 reading manifest file '/tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info/SOURCES.txt' 2024-03-05T18:19:51,539 reading manifest template 'MANIFEST.in' 2024-03-05T18:19:51,597 adding license file 'LICENSE' 2024-03-05T18:19:51,604 writing manifest file '/tmp/pip-pip-egg-info-9bi72nwq/uncalled4.egg-info/SOURCES.txt' 2024-03-05T18:19:51,701 Preparing metadata (setup.py): finished with status 'done' 2024-03-05T18:19:51,716 Source in /tmp/pip-wheel-j_89egjv/uncalled4_c1a18e3e383c4f32879ca8edd0d58ddc has version 4.0.0, which satisfies requirement uncalled4==4.0.0 from https://files.pythonhosted.org/packages/bc/fd/a714f3b65dee9941ca73910515fd77bda3b6813c5832df5d4392221ad64b/uncalled4-4.0.0.tar.gz 2024-03-05T18:19:51,718 Removed uncalled4==4.0.0 from https://files.pythonhosted.org/packages/bc/fd/a714f3b65dee9941ca73910515fd77bda3b6813c5832df5d4392221ad64b/uncalled4-4.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-f9upf843' 2024-03-05T18:19:51,732 Created temporary directory: /tmp/pip-unpack-vk2pzu76 2024-03-05T18:19:51,735 Created temporary directory: /tmp/pip-unpack-7iyo8dk0 2024-03-05T18:19:51,762 Building wheels for collected packages: uncalled4 2024-03-05T18:19:51,788 Created temporary directory: /tmp/pip-wheel-ovbroc7l 2024-03-05T18:19:51,788 Building wheel for uncalled4 (setup.py): started 2024-03-05T18:19:51,790 Destination directory: /tmp/pip-wheel-ovbroc7l 2024-03-05T18:19:51,790 Running command python setup.py bdist_wheel 2024-03-05T18:19:53,231 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-05T18:19:53,231 !! 2024-03-05T18:19:53,231 ******************************************************************************** 2024-03-05T18:19:53,232 Requirements should be satisfied by a PEP 517 installer. 2024-03-05T18:19:53,232 If you are using pip, you can try `pip install --use-pep517`. 2024-03-05T18:19:53,232 ******************************************************************************** 2024-03-05T18:19:53,232 !! 2024-03-05T18:19:53,232 dist.fetch_build_eggs(dist.setup_requires) 2024-03-05T18:19:53,353 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-05T18:19:53,353 warnings.warn(msg) 2024-03-05T18:19:53,734 running bdist_wheel 2024-03-05T18:19:53,927 running build 2024-03-05T18:19:53,927 running build_py 2024-03-05T18:19:54,005 creating build 2024-03-05T18:19:54,008 creating build/lib.linux-armv7l-cpython-39 2024-03-05T18:19:54,014 creating build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,024 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,034 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,045 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,059 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,075 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,091 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,103 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,114 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,124 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,137 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,149 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,155 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,167 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,181 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-05T18:19:54,198 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-05T18:19:54,200 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-05T18:19:54,205 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-05T18:19:54,209 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-05T18:19:54,221 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-05T18:19:54,233 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-05T18:19:54,248 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-05T18:19:54,259 creating build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-05T18:19:54,260 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-05T18:19:54,262 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-05T18:19:54,265 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-05T18:19:54,273 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-05T18:19:54,276 creating build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-05T18:19:54,277 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-05T18:19:54,280 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-05T18:19:54,285 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-05T18:19:54,299 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-05T18:19:54,316 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-05T18:19:54,331 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-05T18:19:54,343 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-05T18:19:54,347 running egg_info 2024-03-05T18:19:54,397 writing src/uncalled4.egg-info/PKG-INFO 2024-03-05T18:19:54,400 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2024-03-05T18:19:54,402 writing entry points to src/uncalled4.egg-info/entry_points.txt 2024-03-05T18:19:54,404 writing requirements to src/uncalled4.egg-info/requires.txt 2024-03-05T18:19:54,405 writing top-level names to src/uncalled4.egg-info/top_level.txt 2024-03-05T18:19:54,437 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-05T18:19:54,448 reading manifest template 'MANIFEST.in' 2024-03-05T18:19:54,500 adding license file 'LICENSE' 2024-03-05T18:19:54,517 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-05T18:19:54,525 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2024-03-05T18:19:54,525 !! 2024-03-05T18:19:54,525 ******************************************************************************** 2024-03-05T18:19:54,526 ############################ 2024-03-05T18:19:54,526 # Package would be ignored # 2024-03-05T18:19:54,526 ############################ 2024-03-05T18:19:54,527 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2024-03-05T18:19:54,527 but it is absent from setuptools' `packages` configuration. 2024-03-05T18:19:54,527 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T18:19:54,528 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2024-03-05T18:19:54,528 to the `packages` configuration field. 2024-03-05T18:19:54,528 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T18:19:54,529 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T18:19:54,529 instead of `find_packages(...)`/`find:`). 2024-03-05T18:19:54,529 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T18:19:54,530 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T18:19:54,530 If you don't want 'uncalled4.__pycache__' to be distributed and are 2024-03-05T18:19:54,531 already explicitly excluding 'uncalled4.__pycache__' via 2024-03-05T18:19:54,531 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T18:19:54,531 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T18:19:54,531 combination with a more fine grained `package-data` configuration. 2024-03-05T18:19:54,532 You can read more about "package data files" on setuptools documentation page: 2024-03-05T18:19:54,532 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T18:19:54,533 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T18:19:54,533 even if it does not contain any `.py` files. 2024-03-05T18:19:54,534 On the other hand, currently there is no concept of package data 2024-03-05T18:19:54,534 directory, all directories are treated like packages. 2024-03-05T18:19:54,534 ******************************************************************************** 2024-03-05T18:19:54,535 !! 2024-03-05T18:19:54,535 check.warn(importable) 2024-03-05T18:19:54,535 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2024-03-05T18:19:54,536 !! 2024-03-05T18:19:54,536 ******************************************************************************** 2024-03-05T18:19:54,536 ############################ 2024-03-05T18:19:54,537 # Package would be ignored # 2024-03-05T18:19:54,537 ############################ 2024-03-05T18:19:54,537 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2024-03-05T18:19:54,537 but it is absent from setuptools' `packages` configuration. 2024-03-05T18:19:54,538 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T18:19:54,538 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2024-03-05T18:19:54,538 to the `packages` configuration field. 2024-03-05T18:19:54,539 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T18:19:54,539 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T18:19:54,539 instead of `find_packages(...)`/`find:`). 2024-03-05T18:19:54,540 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T18:19:54,540 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T18:19:54,541 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2024-03-05T18:19:54,541 already explicitly excluding 'uncalled4.io.__pycache__' via 2024-03-05T18:19:54,541 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T18:19:54,541 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T18:19:54,542 combination with a more fine grained `package-data` configuration. 2024-03-05T18:19:54,542 You can read more about "package data files" on setuptools documentation page: 2024-03-05T18:19:54,543 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T18:19:54,543 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T18:19:54,544 even if it does not contain any `.py` files. 2024-03-05T18:19:54,544 On the other hand, currently there is no concept of package data 2024-03-05T18:19:54,544 directory, all directories are treated like packages. 2024-03-05T18:19:54,544 ******************************************************************************** 2024-03-05T18:19:54,545 !! 2024-03-05T18:19:54,545 check.warn(importable) 2024-03-05T18:19:54,545 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2024-03-05T18:19:54,546 !! 2024-03-05T18:19:54,546 ******************************************************************************** 2024-03-05T18:19:54,546 ############################ 2024-03-05T18:19:54,547 # Package would be ignored # 2024-03-05T18:19:54,547 ############################ 2024-03-05T18:19:54,547 Python recognizes 'uncalled4.models' as an importable package[^1], 2024-03-05T18:19:54,547 but it is absent from setuptools' `packages` configuration. 2024-03-05T18:19:54,548 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T18:19:54,548 package, please make sure that 'uncalled4.models' is explicitly added 2024-03-05T18:19:54,548 to the `packages` configuration field. 2024-03-05T18:19:54,549 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T18:19:54,549 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T18:19:54,549 instead of `find_packages(...)`/`find:`). 2024-03-05T18:19:54,550 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T18:19:54,550 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T18:19:54,551 If you don't want 'uncalled4.models' to be distributed and are 2024-03-05T18:19:54,551 already explicitly excluding 'uncalled4.models' via 2024-03-05T18:19:54,551 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T18:19:54,552 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T18:19:54,552 combination with a more fine grained `package-data` configuration. 2024-03-05T18:19:54,552 You can read more about "package data files" on setuptools documentation page: 2024-03-05T18:19:54,553 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T18:19:54,554 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T18:19:54,554 even if it does not contain any `.py` files. 2024-03-05T18:19:54,554 On the other hand, currently there is no concept of package data 2024-03-05T18:19:54,555 directory, all directories are treated like packages. 2024-03-05T18:19:54,555 ******************************************************************************** 2024-03-05T18:19:54,555 !! 2024-03-05T18:19:54,556 check.warn(importable) 2024-03-05T18:19:54,556 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2024-03-05T18:19:54,556 !! 2024-03-05T18:19:54,557 ******************************************************************************** 2024-03-05T18:19:54,557 ############################ 2024-03-05T18:19:54,557 # Package would be ignored # 2024-03-05T18:19:54,558 ############################ 2024-03-05T18:19:54,558 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2024-03-05T18:19:54,558 but it is absent from setuptools' `packages` configuration. 2024-03-05T18:19:54,559 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T18:19:54,559 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2024-03-05T18:19:54,559 to the `packages` configuration field. 2024-03-05T18:19:54,560 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T18:19:54,560 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T18:19:54,560 instead of `find_packages(...)`/`find:`). 2024-03-05T18:19:54,561 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T18:19:54,561 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T18:19:54,562 If you don't want 'uncalled4.models.tombo' to be distributed and are 2024-03-05T18:19:54,562 already explicitly excluding 'uncalled4.models.tombo' via 2024-03-05T18:19:54,563 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T18:19:54,563 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T18:19:54,563 combination with a more fine grained `package-data` configuration. 2024-03-05T18:19:54,564 You can read more about "package data files" on setuptools documentation page: 2024-03-05T18:19:54,564 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T18:19:54,565 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T18:19:54,565 even if it does not contain any `.py` files. 2024-03-05T18:19:54,566 On the other hand, currently there is no concept of package data 2024-03-05T18:19:54,566 directory, all directories are treated like packages. 2024-03-05T18:19:54,566 ******************************************************************************** 2024-03-05T18:19:54,567 !! 2024-03-05T18:19:54,567 check.warn(importable) 2024-03-05T18:19:54,567 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2024-03-05T18:19:54,567 !! 2024-03-05T18:19:54,568 ******************************************************************************** 2024-03-05T18:19:54,568 ############################ 2024-03-05T18:19:54,568 # Package would be ignored # 2024-03-05T18:19:54,569 ############################ 2024-03-05T18:19:54,569 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2024-03-05T18:19:54,569 but it is absent from setuptools' `packages` configuration. 2024-03-05T18:19:54,570 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T18:19:54,570 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2024-03-05T18:19:54,570 to the `packages` configuration field. 2024-03-05T18:19:54,571 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T18:19:54,571 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T18:19:54,571 instead of `find_packages(...)`/`find:`). 2024-03-05T18:19:54,572 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T18:19:54,573 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T18:19:54,573 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2024-03-05T18:19:54,574 already explicitly excluding 'uncalled4.stats.__pycache__' via 2024-03-05T18:19:54,574 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T18:19:54,574 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T18:19:54,574 combination with a more fine grained `package-data` configuration. 2024-03-05T18:19:54,575 You can read more about "package data files" on setuptools documentation page: 2024-03-05T18:19:54,575 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T18:19:54,576 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T18:19:54,577 even if it does not contain any `.py` files. 2024-03-05T18:19:54,577 On the other hand, currently there is no concept of package data 2024-03-05T18:19:54,577 directory, all directories are treated like packages. 2024-03-05T18:19:54,577 ******************************************************************************** 2024-03-05T18:19:54,578 !! 2024-03-05T18:19:54,578 check.warn(importable) 2024-03-05T18:19:54,579 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2024-03-05T18:19:54,579 !! 2024-03-05T18:19:54,580 ******************************************************************************** 2024-03-05T18:19:54,580 ############################ 2024-03-05T18:19:54,581 # Package would be ignored # 2024-03-05T18:19:54,581 ############################ 2024-03-05T18:19:54,581 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2024-03-05T18:19:54,582 but it is absent from setuptools' `packages` configuration. 2024-03-05T18:19:54,583 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T18:19:54,583 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2024-03-05T18:19:54,583 to the `packages` configuration field. 2024-03-05T18:19:54,584 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T18:19:54,584 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T18:19:54,585 instead of `find_packages(...)`/`find:`). 2024-03-05T18:19:54,585 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T18:19:54,586 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T18:19:54,587 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2024-03-05T18:19:54,587 already explicitly excluding 'uncalled4.vis.__pycache__' via 2024-03-05T18:19:54,587 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T18:19:54,588 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T18:19:54,588 combination with a more fine grained `package-data` configuration. 2024-03-05T18:19:54,588 You can read more about "package data files" on setuptools documentation page: 2024-03-05T18:19:54,589 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T18:19:54,590 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T18:19:54,590 even if it does not contain any `.py` files. 2024-03-05T18:19:54,590 On the other hand, currently there is no concept of package data 2024-03-05T18:19:54,591 directory, all directories are treated like packages. 2024-03-05T18:19:54,591 ******************************************************************************** 2024-03-05T18:19:54,592 !! 2024-03-05T18:19:54,592 check.warn(importable) 2024-03-05T18:19:54,592 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2024-03-05T18:19:54,592 !! 2024-03-05T18:19:54,593 ******************************************************************************** 2024-03-05T18:19:54,593 ############################ 2024-03-05T18:19:54,593 # Package would be ignored # 2024-03-05T18:19:54,594 ############################ 2024-03-05T18:19:54,594 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2024-03-05T18:19:54,595 but it is absent from setuptools' `packages` configuration. 2024-03-05T18:19:54,595 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T18:19:54,595 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2024-03-05T18:19:54,596 to the `packages` configuration field. 2024-03-05T18:19:54,596 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T18:19:54,596 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T18:19:54,597 instead of `find_packages(...)`/`find:`). 2024-03-05T18:19:54,597 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T18:19:54,598 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T18:19:54,598 If you don't want 'uncalled4.vis.assets' to be distributed and are 2024-03-05T18:19:54,599 already explicitly excluding 'uncalled4.vis.assets' via 2024-03-05T18:19:54,599 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T18:19:54,599 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T18:19:54,599 combination with a more fine grained `package-data` configuration. 2024-03-05T18:19:54,600 You can read more about "package data files" on setuptools documentation page: 2024-03-05T18:19:54,601 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T18:19:54,601 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T18:19:54,602 even if it does not contain any `.py` files. 2024-03-05T18:19:54,602 On the other hand, currently there is no concept of package data 2024-03-05T18:19:54,602 directory, all directories are treated like packages. 2024-03-05T18:19:54,603 ******************************************************************************** 2024-03-05T18:19:54,603 !! 2024-03-05T18:19:54,603 check.warn(importable) 2024-03-05T18:19:54,603 creating build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,603 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,604 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,604 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,604 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,604 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,604 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,604 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,605 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,605 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,605 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,605 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,605 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,606 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,609 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,611 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,614 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,616 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,618 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,623 copying src/uncalled4/__pycache__/train.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-05T18:19:54,625 creating build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-05T18:19:54,626 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-05T18:19:54,628 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-05T18:19:54,798 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-05T18:19:54,802 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-05T18:19:54,805 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-05T18:19:54,808 creating build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-05T18:19:54,809 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-05T18:19:54,813 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-05T18:19:54,815 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,817 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,819 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,821 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,824 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,827 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,830 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,832 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,835 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,838 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,841 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,845 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,854 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,856 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,859 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,862 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-05T18:19:54,864 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-05T18:19:54,865 copying src/uncalled4/vis/assets/.browser.js.swp -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-05T18:19:54,868 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-05T18:19:54,870 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-05T18:19:54,873 creating build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,874 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,876 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,878 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,882 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,886 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,888 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,891 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,894 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,898 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,900 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,902 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,905 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,907 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,910 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-05T18:19:54,912 creating build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,913 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,916 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,919 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,922 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,925 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,927 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,930 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,933 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,936 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,939 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-05T18:19:54,944 running build_ext 2024-03-05T18:19:55,520 building '_uncalled4' extension 2024-03-05T18:19:55,521 creating build/temp.linux-armv7l-cpython-39 2024-03-05T18:19:55,521 creating build/temp.linux-armv7l-cpython-39/src 2024-03-05T18:19:55,522 creating build/temp.linux-armv7l-cpython-39/src/cpp 2024-03-05T18:19:55,556 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/config.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/config.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:19:55,558 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/dtw.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/dtw.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:19:55,558 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/event_detector.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/event_detector.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:19:55,561 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/intervals.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/intervals.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:20:02,661 In file included from src/cpp/event_detector.cpp:15: 2024-03-05T18:20:02,662 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-05T18:20:02,663 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:20:02,663 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-05T18:20:02,663 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-05T18:20:02,664 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:20:02,664 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-05T18:20:02,685 In file included from src/cpp/aln.hpp:11, 2024-03-05T18:20:02,686 from src/cpp/dtw.hpp:9, 2024-03-05T18:20:02,686 from src/cpp/config.hpp:30, 2024-03-05T18:20:02,687 from src/cpp/config.cpp:1: 2024-03-05T18:20:02,687 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-05T18:20:02,687 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:20:02,687 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-05T18:20:02,688 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-05T18:20:02,688 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:20:02,688 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-05T18:20:02,703 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-05T18:20:02,704 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-05T18:20:02,704 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-05T18:20:02,705 | ~~^~~~~~~~~~ 2024-03-05T18:20:02,705 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-05T18:20:02,705 src/cpp/event_detector.hpp:158:34: warning: narrowing conversion of ‘((ProcessedRead*)this)->ProcessedRead::events.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-05T18:20:02,706 158 | normalize({0, events.size(), scale, shift}); 2024-03-05T18:20:02,706 | ~~~~~~~~~~~^~ 2024-03-05T18:20:02,744 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-05T18:20:02,744 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-05T18:20:02,745 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-05T18:20:02,745 | ~~^~~~~~~~~~ 2024-03-05T18:20:02,745 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-05T18:20:02,746 src/cpp/event_detector.hpp:158:34: warning: narrowing conversion of ‘((ProcessedRead*)this)->ProcessedRead::events.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-05T18:20:02,746 158 | normalize({0, events.size(), scale, shift}); 2024-03-05T18:20:02,746 | ~~~~~~~~~~~^~ 2024-03-05T18:20:02,802 In file included from src/cpp/aln.hpp:11, 2024-03-05T18:20:02,803 from src/cpp/dtw.hpp:9, 2024-03-05T18:20:02,803 from src/cpp/dtw.cpp:1: 2024-03-05T18:20:02,803 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-05T18:20:02,804 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:20:02,804 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-05T18:20:02,804 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-05T18:20:02,805 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:20:02,805 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-05T18:20:02,865 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-05T18:20:02,866 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-05T18:20:02,866 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-05T18:20:02,867 | ~~^~~~~~~~~~ 2024-03-05T18:20:02,868 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-05T18:20:02,868 src/cpp/event_detector.hpp:158:34: warning: narrowing conversion of ‘((ProcessedRead*)this)->ProcessedRead::events.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-05T18:20:02,869 158 | normalize({0, events.size(), scale, shift}); 2024-03-05T18:20:02,869 | ~~~~~~~~~~~^~ 2024-03-05T18:20:02,934 In file included from src/cpp/dtw.hpp:9, 2024-03-05T18:20:02,934 from src/cpp/config.hpp:30, 2024-03-05T18:20:02,935 from src/cpp/config.cpp:1: 2024-03-05T18:20:02,935 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-05T18:20:02,935 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-05T18:20:02,935 187 | i64 ref; 2024-03-05T18:20:02,936 | ^~~ 2024-03-05T18:20:02,939 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-05T18:20:02,940 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-05T18:20:02,940 279 | int len,dist; 2024-03-05T18:20:02,940 | ^~~~ 2024-03-05T18:20:03,048 In file included from src/cpp/dtw.hpp:9, 2024-03-05T18:20:03,048 from src/cpp/dtw.cpp:1: 2024-03-05T18:20:03,049 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-05T18:20:03,049 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-05T18:20:03,049 187 | i64 ref; 2024-03-05T18:20:03,050 | ^~~ 2024-03-05T18:20:03,056 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-05T18:20:03,056 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-05T18:20:03,056 279 | int len,dist; 2024-03-05T18:20:03,057 | ^~~~ 2024-03-05T18:20:03,220 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2024-03-05T18:20:03,220 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2024-03-05T18:20:03,221 21 | size_t i = 0, j = 0, b = 0; 2024-03-05T18:20:03,221 | ^ 2024-03-05T18:20:03,235 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2024-03-05T18:20:03,236 src/cpp/dtw.cpp:98:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2024-03-05T18:20:03,236 98 | auto fill = backfill_na ? samps : Interval(); 2024-03-05T18:20:03,236 | ^~~~ 2024-03-05T18:20:05,179 In file included from src/cpp/intervals.cpp:2: 2024-03-05T18:20:05,179 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2024-03-05T18:20:05,180 src/cpp/intervals.hpp:467:31: required from ‘static void IntervalIndex::pybind(pybind11::module_&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:20:05,180 src/cpp/intervals.cpp:7:25: required from here 2024-03-05T18:20:05,180 src/cpp/intervals.hpp:348:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2024-03-05T18:20:05,181 348 | while (gap >= MAX_LEN_I16) { 2024-03-05T18:20:05,181 | ~~~~^~~~~~~~~~~~~~ 2024-03-05T18:20:26,607 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/normalizer.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/normalizer.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:20:36,658 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/pore_model.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/pore_model.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:20:43,581 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/pybinder.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/pybinder.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:20:49,856 In file included from /usr/include/c++/10/vector:72, 2024-03-05T18:20:49,857 from src/cpp/intervals.hpp:6, 2024-03-05T18:20:49,860 from src/cpp/intervals.cpp:2: 2024-03-05T18:20:49,860 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Interval&}; _Tp = Interval; _Alloc = std::allocator >]’: 2024-03-05T18:20:49,861 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-03-05T18:20:49,861 426 | vector<_Tp, _Alloc>:: 2024-03-05T18:20:49,862 | ^~~~~~~~~~~~~~~~~~~ 2024-03-05T18:20:50,006 In file included from /usr/include/c++/10/vector:67, 2024-03-05T18:20:50,006 from src/cpp/intervals.hpp:6, 2024-03-05T18:20:50,007 from src/cpp/intervals.cpp:2: 2024-03-05T18:20:50,007 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::mirror() const [with T = long long int]’: 2024-03-05T18:20:50,008 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:20:50,008 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:20:50,009 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:20:50,111 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’: 2024-03-05T18:20:50,111 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:20:50,112 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:20:50,112 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:20:50,112 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:20:50,113 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:20:50,113 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:20:50,261 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::intersect(IntervalIndex) const [with T = long long int]’: 2024-03-05T18:20:50,262 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:20:50,262 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:20:50,262 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:20:50,420 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’: 2024-03-05T18:20:50,421 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:20:50,421 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:20:50,421 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:20:50,422 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:20:50,422 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:20:50,422 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:20:50,423 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:20:50,423 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:20:50,423 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:20:58,358 In file included from src/cpp/signal_processor.hpp:7, 2024-03-05T18:20:58,358 from src/cpp/pybinder.cpp:6: 2024-03-05T18:20:58,359 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-05T18:20:58,359 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:20:58,360 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-05T18:20:58,360 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-05T18:20:58,361 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:20:58,361 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-05T18:20:58,412 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-05T18:20:58,412 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-05T18:20:58,413 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-05T18:20:58,413 | ~~^~~~~~~~~~ 2024-03-05T18:20:58,413 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-05T18:20:58,414 src/cpp/event_detector.hpp:158:34: warning: narrowing conversion of ‘((ProcessedRead*)this)->ProcessedRead::events.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-05T18:20:58,414 158 | normalize({0, events.size(), scale, shift}); 2024-03-05T18:20:58,415 | ~~~~~~~~~~~^~ 2024-03-05T18:20:59,022 In file included from src/cpp/dtw.hpp:9, 2024-03-05T18:20:59,022 from src/cpp/pybinder.cpp:8: 2024-03-05T18:20:59,023 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-05T18:20:59,023 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-05T18:20:59,023 187 | i64 ref; 2024-03-05T18:20:59,024 | ^~~ 2024-03-05T18:20:59,028 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-05T18:20:59,029 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-05T18:20:59,029 279 | int len,dist; 2024-03-05T18:20:59,029 | ^~~~ 2024-03-05T18:21:05,357 In file included from /usr/include/c++/10/vector:72, 2024-03-05T18:21:05,357 from src/cpp/intervals.hpp:6, 2024-03-05T18:21:05,358 from src/cpp/intervals.cpp:2: 2024-03-05T18:21:05,358 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: 2024-03-05T18:21:05,358 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-03-05T18:21:05,359 426 | vector<_Tp, _Alloc>:: 2024-03-05T18:21:05,359 | ^~~~~~~~~~~~~~~~~~~ 2024-03-05T18:21:05,462 /usr/include/c++/10/bits/vector.tcc: In member function ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector, std::allocator > >; Value = std::pair]’: 2024-03-05T18:21:05,462 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:21:05,462 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-03-05T18:21:05,463 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-05T18:21:05,493 In file included from src/cpp/pybinder.cpp:10: 2024-03-05T18:21:05,493 src/cpp/eventalign.hpp: In instantiation of ‘std::string write_eventalign_new(Alignment&, bool, bool, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’: 2024-03-05T18:21:05,493 src/cpp/pybinder.cpp:34:10: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:05,494 src/cpp/pybinder.cpp:66:31: required from here 2024-03-05T18:21:05,494 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:21:05,495 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-05T18:21:05,495 | ~~^~~~~~~~~~~ 2024-03-05T18:21:05,758 In file included from /usr/include/c++/10/vector:67, 2024-03-05T18:21:05,759 from src/cpp/intervals.hpp:6, 2024-03-05T18:21:05,759 from src/cpp/intervals.cpp:2: 2024-03-05T18:21:05,759 /usr/include/c++/10/bits/stl_vector.h: In static member function ‘static pybind11::handle pybind11::cpp_function::initialize::execute >, {}, 0>::, std::allocator > >)>, void, {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}, {pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor}>::::_FUN(pybind11::detail::function_call&)’: 2024-03-05T18:21:05,760 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:21:05,760 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:21:05,760 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:21:05,761 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-05T18:21:05,761 1198 | _M_realloc_insert(end(), __x); 2024-03-05T18:21:05,762 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T18:21:05,802 src/cpp/eventalign.hpp: In instantiation of ‘std::string write_eventalign_new(Alignment&, bool, bool, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’: 2024-03-05T18:21:05,803 src/cpp/pybinder.cpp:34:10: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:05,803 src/cpp/pybinder.cpp:67:31: required from here 2024-03-05T18:21:05,803 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T18:21:16,842 In file included from src/cpp/pybinder.cpp:8: 2024-03-05T18:21:16,843 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-05T18:21:16,843 src/cpp/dtw.hpp:734:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:16,843 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:16,844 src/cpp/pybinder.cpp:66:31: required from here 2024-03-05T18:21:16,844 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T18:21:16,844 644 | if (q0 >= qry_size()) { 2024-03-05T18:21:16,844 | ~~~^~~~~~~~~~~~~ 2024-03-05T18:21:16,845 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T18:21:16,846 651 | if (r1 > ref_size()) { 2024-03-05T18:21:16,846 | ~~~^~~~~~~~~~~~ 2024-03-05T18:21:17,769 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-05T18:21:17,769 src/cpp/dtw.hpp:734:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:17,769 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:17,770 src/cpp/pybinder.cpp:67:31: required from here 2024-03-05T18:21:17,770 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T18:21:17,770 644 | if (q0 >= qry_size()) { 2024-03-05T18:21:17,771 | ~~~^~~~~~~~~~~~~ 2024-03-05T18:21:17,771 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T18:21:17,772 651 | if (r1 > ref_size()) { 2024-03-05T18:21:17,772 | ~~~^~~~~~~~~~~~ 2024-03-05T18:21:19,828 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/read_buffer.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/read_buffer.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:21:24,706 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/util.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/util.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-05T18:21:33,434 In file included from src/cpp/seq.hpp:32, 2024-03-05T18:21:33,434 from src/cpp/pybinder.cpp:7: 2024-03-05T18:21:33,434 src/cpp/pore_model.hpp: In instantiation of ‘DestIter PoreModel::str_to_kmers(StrIter, DestIter, size_t, KmerType, bool) const [with StrIter = __gnu_cxx::__normal_iterator >; DestIter = short unsigned int*; KmerType = short unsigned int; size_t = unsigned int]’: 2024-03-05T18:21:33,435 src/cpp/pore_model.hpp:496:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:33,435 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:33,435 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:33,436 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:33,436 src/cpp/pybinder.cpp:66:31: required from here 2024-03-05T18:21:33,436 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-05T18:21:33,437 507 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2024-03-05T18:21:33,437 | ~~~~~~~~~~^ 2024-03-05T18:21:33,441 src/cpp/pore_model.hpp: In instantiation of ‘DestIter PoreModel::str_to_kmers(StrIter, DestIter, size_t, KmerType, bool) const [with StrIter = std::reverse_iterator<__gnu_cxx::__normal_iterator > >; DestIter = short unsigned int*; KmerType = short unsigned int; size_t = unsigned int]’: 2024-03-05T18:21:33,441 src/cpp/pore_model.hpp:498:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:33,442 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:33,442 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:33,443 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:33,443 src/cpp/pybinder.cpp:66:31: required from here 2024-03-05T18:21:33,443 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-05T18:21:39,230 src/cpp/pore_model.hpp: In instantiation of ‘DestIter PoreModel::str_to_kmers(StrIter, DestIter, size_t, KmerType, bool) const [with StrIter = __gnu_cxx::__normal_iterator >; DestIter = unsigned int*; KmerType = unsigned int; size_t = unsigned int]’: 2024-03-05T18:21:39,230 src/cpp/pore_model.hpp:496:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:39,230 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:39,230 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:39,231 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:39,231 src/cpp/pybinder.cpp:67:31: required from here 2024-03-05T18:21:39,232 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-05T18:21:39,232 src/cpp/pore_model.hpp: In instantiation of ‘DestIter PoreModel::str_to_kmers(StrIter, DestIter, size_t, KmerType, bool) const [with StrIter = std::reverse_iterator<__gnu_cxx::__normal_iterator > >; DestIter = unsigned int*; KmerType = unsigned int; size_t = unsigned int]’: 2024-03-05T18:21:39,232 src/cpp/pore_model.hpp:498:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:39,233 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:39,233 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:39,233 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:39,234 src/cpp/pybinder.cpp:67:31: required from here 2024-03-05T18:21:39,234 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-05T18:21:45,211 src/cpp/pore_model.hpp: In instantiation of ‘void PoreModel::init_current(const Container&, const Container&, const Container&, const Container&, bool) [with Container = PyArray; KmerType = short unsigned int]’: 2024-03-05T18:21:45,212 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-05T18:21:45,212 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-05T18:21:45,212 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-05T18:21:45,213 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-05T18:21:45,213 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:45,214 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:45,214 src/cpp/pybinder.cpp:66:31: required from here 2024-03-05T18:21:45,214 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-05T18:21:45,214 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-05T18:21:45,215 | ^~~~~~~~ 2024-03-05T18:21:46,139 In file included from src/cpp/pybinder.cpp:8: 2024-03-05T18:21:46,140 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-05T18:21:46,140 src/cpp/dtw.hpp:356:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = short unsigned int]’ 2024-03-05T18:21:46,140 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-05T18:21:46,141 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-05T18:21:46,141 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-05T18:21:46,141 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:46,142 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:46,142 src/cpp/pybinder.cpp:66:31: required from here 2024-03-05T18:21:46,142 src/cpp/dtw.hpp:443:33: warning: comparison of integer expressions of different signedness: ‘i32’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T18:21:46,142 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-05T18:21:46,143 | ~~^~~~~~~~~~~~ 2024-03-05T18:21:46,143 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-05T18:21:46,144 src/cpp/dtw.hpp:357:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = short unsigned int]’ 2024-03-05T18:21:46,144 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-05T18:21:46,145 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-05T18:21:46,145 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-05T18:21:46,145 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:46,145 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:46,146 src/cpp/pybinder.cpp:66:31: required from here 2024-03-05T18:21:46,146 src/cpp/dtw.hpp:507:46: warning: narrowing conversion of ‘(((size_t)(path_ll.Coord::qry - offs)) + ((BandedDTW >*)this)->BandedDTW >::event_start_)’ from ‘size_t’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-05T18:21:46,146 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-05T18:21:46,147 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-05T18:21:47,279 In file included from src/cpp/seq.hpp:32, 2024-03-05T18:21:47,279 from src/cpp/pybinder.cpp:7: 2024-03-05T18:21:47,280 src/cpp/pore_model.hpp: In instantiation of ‘void PoreModel::init_current(const Container&, const Container&, const Container&, const Container&, bool) [with Container = PyArray; KmerType = unsigned int]’: 2024-03-05T18:21:47,280 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2024-03-05T18:21:47,281 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-05T18:21:47,281 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-05T18:21:47,281 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-05T18:21:47,282 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:47,282 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:47,282 src/cpp/pybinder.cpp:67:31: required from here 2024-03-05T18:21:47,283 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-05T18:21:47,283 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-05T18:21:47,283 | ^~~~~~~~ 2024-03-05T18:21:47,490 In file included from src/cpp/pybinder.cpp:8: 2024-03-05T18:21:47,490 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-05T18:21:47,491 src/cpp/dtw.hpp:356:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = unsigned int]’ 2024-03-05T18:21:47,491 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-05T18:21:47,491 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-05T18:21:47,492 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-05T18:21:47,492 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:47,492 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:47,493 src/cpp/pybinder.cpp:67:31: required from here 2024-03-05T18:21:47,493 src/cpp/dtw.hpp:443:33: warning: comparison of integer expressions of different signedness: ‘i32’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T18:21:47,493 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-05T18:21:47,494 | ~~^~~~~~~~~~~~ 2024-03-05T18:21:47,494 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-05T18:21:47,495 src/cpp/dtw.hpp:357:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = unsigned int]’ 2024-03-05T18:21:47,495 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-05T18:21:47,495 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-05T18:21:47,496 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-05T18:21:47,496 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:47,496 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:47,497 src/cpp/pybinder.cpp:67:31: required from here 2024-03-05T18:21:47,497 src/cpp/dtw.hpp:507:46: warning: narrowing conversion of ‘(((size_t)(path_ll.Coord::qry - offs)) + ((BandedDTW >*)this)->BandedDTW >::event_start_)’ from ‘size_t’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-05T18:21:47,497 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-05T18:21:47,498 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-05T18:21:49,548 In file included from src/cpp/read_buffer.hpp:30, 2024-03-05T18:21:49,548 from src/cpp/pybinder.cpp:5: 2024-03-05T18:21:49,548 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2024-03-05T18:21:49,549 src/cpp/pore_model.hpp:369:45: required from ‘void PoreModel::init_current(const Container&, const Container&, const Container&, const Container&, bool) [with Container = PyArray; KmerType = short unsigned int]’ 2024-03-05T18:21:49,549 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-05T18:21:49,549 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-05T18:21:49,550 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-05T18:21:49,550 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-05T18:21:49,550 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:49,551 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-05T18:21:49,551 src/cpp/pybinder.cpp:66:31: required from here 2024-03-05T18:21:49,551 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2024-03-05T18:21:49,551 144 | auto sum = super::sum(); 2024-03-05T18:21:49,552 | ^~~ 2024-03-05T18:21:49,552 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2024-03-05T18:21:49,552 145 | auto len = super::size(); 2024-03-05T18:21:49,552 | ^~~ 2024-03-05T18:22:08,055 virtual memory exhausted: Cannot allocate memory 2024-03-05T18:22:08,179 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-03-05T18:22:54,693 ERROR: python setup.py bdist_wheel exited with 1 2024-03-05T18:22:54,711 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2024-03-05T18:22:54,711 exec(compile('"'"''"'"''"'"' 2024-03-05T18:22:54,711 # This is -- a caller that pip uses to run setup.py 2024-03-05T18:22:54,711 # 2024-03-05T18:22:54,711 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-03-05T18:22:54,711 # import from `distutils.core` to work with newer packaging standards. 2024-03-05T18:22:54,711 # - It provides a clear error message when setuptools is not installed. 2024-03-05T18:22:54,711 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-03-05T18:22:54,711 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-03-05T18:22:54,711 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-03-05T18:22:54,711 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-03-05T18:22:54,711 import os, sys, tokenize 2024-03-05T18:22:54,711 2024-03-05T18:22:54,711 try: 2024-03-05T18:22:54,711 import setuptools 2024-03-05T18:22:54,711 except ImportError as error: 2024-03-05T18:22:54,711 print( 2024-03-05T18:22:54,711 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-03-05T18:22:54,711 "the build environment.", 2024-03-05T18:22:54,711 file=sys.stderr, 2024-03-05T18:22:54,711 ) 2024-03-05T18:22:54,711 sys.exit(1) 2024-03-05T18:22:54,711 2024-03-05T18:22:54,711 __file__ = %r 2024-03-05T18:22:54,711 sys.argv[0] = __file__ 2024-03-05T18:22:54,711 2024-03-05T18:22:54,711 if os.path.exists(__file__): 2024-03-05T18:22:54,711 filename = __file__ 2024-03-05T18:22:54,711 with tokenize.open(__file__) as f: 2024-03-05T18:22:54,711 setup_py_code = f.read() 2024-03-05T18:22:54,711 else: 2024-03-05T18:22:54,711 filename = "" 2024-03-05T18:22:54,711 setup_py_code = "from setuptools import setup; setup()" 2024-03-05T18:22:54,711 2024-03-05T18:22:54,711 exec(compile(setup_py_code, filename, "exec")) 2024-03-05T18:22:54,711 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-j_89egjv/uncalled4_c1a18e3e383c4f32879ca8edd0d58ddc/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ovbroc7l[/] 2024-03-05T18:22:54,711 [bold magenta]cwd[/]: /tmp/pip-wheel-j_89egjv/uncalled4_c1a18e3e383c4f32879ca8edd0d58ddc/ 2024-03-05T18:22:54,711 Building wheel for uncalled4 (setup.py): finished with status 'error' 2024-03-05T18:22:54,712 ERROR: Failed building wheel for uncalled4 2024-03-05T18:22:54,713 Running setup.py clean for uncalled4 2024-03-05T18:22:54,714 Running command python setup.py clean 2024-03-05T18:22:55,663 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-05T18:22:55,663 !! 2024-03-05T18:22:55,664 ******************************************************************************** 2024-03-05T18:22:55,664 Requirements should be satisfied by a PEP 517 installer. 2024-03-05T18:22:55,664 If you are using pip, you can try `pip install --use-pep517`. 2024-03-05T18:22:55,664 ******************************************************************************** 2024-03-05T18:22:55,664 !! 2024-03-05T18:22:55,664 dist.fetch_build_eggs(dist.setup_requires) 2024-03-05T18:22:55,737 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-05T18:22:55,738 warnings.warn(msg) 2024-03-05T18:22:55,909 running clean 2024-03-05T18:22:55,959 removing 'build/temp.linux-armv7l-cpython-39' (and everything under it) 2024-03-05T18:22:55,984 removing 'build/lib.linux-armv7l-cpython-39' (and everything under it) 2024-03-05T18:22:56,041 'build/bdist.linux-armv7l' does not exist -- can't clean it 2024-03-05T18:22:56,042 'build/scripts-3.9' does not exist -- can't clean it 2024-03-05T18:22:56,042 removing 'build' 2024-03-05T18:22:56,136 Failed to build uncalled4 2024-03-05T18:22:56,137 ERROR: Failed to build one or more wheels 2024-03-05T18:22:56,139 Exception information: 2024-03-05T18:22:56,139 Traceback (most recent call last): 2024-03-05T18:22:56,139 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2024-03-05T18:22:56,139 status = run_func(*args) 2024-03-05T18:22:56,139 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2024-03-05T18:22:56,139 return func(self, options, args) 2024-03-05T18:22:56,139 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 181, in run 2024-03-05T18:22:56,139 raise CommandError("Failed to build one or more wheels") 2024-03-05T18:22:56,139 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-03-05T18:22:56,142 Removed build tracker: '/tmp/pip-build-tracker-f9upf843'