2024-03-21T21:05:48,235 Created temporary directory: /tmp/pip-build-tracker-zo10dc4v 2024-03-21T21:05:48,237 Initialized build tracking at /tmp/pip-build-tracker-zo10dc4v 2024-03-21T21:05:48,237 Created build tracker: /tmp/pip-build-tracker-zo10dc4v 2024-03-21T21:05:48,237 Entered build tracker: /tmp/pip-build-tracker-zo10dc4v 2024-03-21T21:05:48,238 Created temporary directory: /tmp/pip-wheel-6_elnzuc 2024-03-21T21:05:48,242 Created temporary directory: /tmp/pip-ephem-wheel-cache-55s2qsny 2024-03-21T21:05:48,265 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-21T21:05:48,269 2 location(s) to search for versions of uncalled4: 2024-03-21T21:05:48,269 * https://pypi.org/simple/uncalled4/ 2024-03-21T21:05:48,269 * https://www.piwheels.org/simple/uncalled4/ 2024-03-21T21:05:48,269 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2024-03-21T21:05:48,270 Getting page https://pypi.org/simple/uncalled4/ 2024-03-21T21:05:48,272 Found index url https://pypi.org/simple/ 2024-03-21T21:05:48,324 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2024-03-21T21:05:48,325 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 2024-03-21T21:05:48,326 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 2024-03-21T21:05:48,326 Found link https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz (from https://pypi.org/simple/uncalled4/) (requires-python:>=3.8), version: 4.0.1 2024-03-21T21:05:48,327 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2024-03-21T21:05:48,327 Getting page https://www.piwheels.org/simple/uncalled4/ 2024-03-21T21:05:48,328 Found index url https://www.piwheels.org/simple/ 2024-03-21T21:05:48,572 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2024-03-21T21:05:48,573 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2024-03-21T21:05:48,574 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2024-03-21T21:05:48,590 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2024-03-21T21:05:48,605 Collecting uncalled4==4.0.1 2024-03-21T21:05:48,607 Created temporary directory: /tmp/pip-unpack-usup76u5 2024-03-21T21:05:48,658 Downloading uncalled4-4.0.1.tar.gz (19.2 MB) 2024-03-21T21:05:52,183 Added uncalled4==4.0.1 from https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-zo10dc4v' 2024-03-21T21:05:52,185 Running setup.py (path:/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/setup.py) egg_info for package uncalled4 2024-03-21T21:05:52,186 Created temporary directory: /tmp/pip-pip-egg-info-pn473w49 2024-03-21T21:05:52,186 Preparing metadata (setup.py): started 2024-03-21T21:05:52,187 Running command python setup.py egg_info 2024-03-21T21:05:53,376 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-21T21:05:53,377 !! 2024-03-21T21:05:53,377 ******************************************************************************** 2024-03-21T21:05:53,377 Requirements should be satisfied by a PEP 517 installer. 2024-03-21T21:05:53,378 If you are using pip, you can try `pip install --use-pep517`. 2024-03-21T21:05:53,378 ******************************************************************************** 2024-03-21T21:05:53,378 !! 2024-03-21T21:05:53,378 dist.fetch_build_eggs(dist.setup_requires) 2024-03-21T21:05:57,767 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-21T21:05:57,768 warnings.warn(msg) 2024-03-21T21:05:57,864 running egg_info 2024-03-21T21:05:57,866 creating /tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info 2024-03-21T21:05:57,893 writing /tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info/PKG-INFO 2024-03-21T21:05:57,898 writing dependency_links to /tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info/dependency_links.txt 2024-03-21T21:05:57,900 writing entry points to /tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info/entry_points.txt 2024-03-21T21:05:57,902 writing requirements to /tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info/requires.txt 2024-03-21T21:05:57,904 writing top-level names to /tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info/top_level.txt 2024-03-21T21:05:57,905 writing manifest file '/tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info/SOURCES.txt' 2024-03-21T21:05:58,035 reading manifest file '/tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info/SOURCES.txt' 2024-03-21T21:05:58,036 reading manifest template 'MANIFEST.in' 2024-03-21T21:05:58,109 adding license file 'LICENSE' 2024-03-21T21:05:58,116 writing manifest file '/tmp/pip-pip-egg-info-pn473w49/uncalled4.egg-info/SOURCES.txt' 2024-03-21T21:05:58,211 Preparing metadata (setup.py): finished with status 'done' 2024-03-21T21:05:58,217 Source in /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac has version 4.0.1, which satisfies requirement uncalled4==4.0.1 from https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz 2024-03-21T21:05:58,218 Removed uncalled4==4.0.1 from https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-zo10dc4v' 2024-03-21T21:05:58,224 Created temporary directory: /tmp/pip-unpack-nnzrqzgh 2024-03-21T21:05:58,225 Created temporary directory: /tmp/pip-unpack-pac_yp8c 2024-03-21T21:05:58,242 Building wheels for collected packages: uncalled4 2024-03-21T21:05:58,246 Created temporary directory: /tmp/pip-wheel-lix5f3cg 2024-03-21T21:05:58,247 Building wheel for uncalled4 (setup.py): started 2024-03-21T21:05:58,248 Destination directory: /tmp/pip-wheel-lix5f3cg 2024-03-21T21:05:58,248 Running command python setup.py bdist_wheel 2024-03-21T21:06:02,371 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-21T21:06:02,372 !! 2024-03-21T21:06:02,373 ******************************************************************************** 2024-03-21T21:06:02,373 Requirements should be satisfied by a PEP 517 installer. 2024-03-21T21:06:02,374 If you are using pip, you can try `pip install --use-pep517`. 2024-03-21T21:06:02,374 ******************************************************************************** 2024-03-21T21:06:02,375 !! 2024-03-21T21:06:02,375 dist.fetch_build_eggs(dist.setup_requires) 2024-03-21T21:06:02,638 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-21T21:06:02,638 warnings.warn(msg) 2024-03-21T21:06:02,803 running bdist_wheel 2024-03-21T21:06:02,913 running build 2024-03-21T21:06:02,913 running build_py 2024-03-21T21:06:02,944 creating build 2024-03-21T21:06:02,945 creating build/lib.linux-armv7l-cpython-39 2024-03-21T21:06:02,946 creating build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,948 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,951 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,954 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,956 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,960 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,962 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,965 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,967 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,969 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,972 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,975 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,977 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,980 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,983 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-21T21:06:02,993 creating build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-21T21:06:03,006 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-21T21:06:03,539 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-21T21:06:04,194 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-21T21:06:04,216 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-21T21:06:04,221 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-21T21:06:04,223 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-21T21:06:04,227 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-21T21:06:04,232 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-21T21:06:04,236 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-21T21:06:04,240 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-21T21:06:04,245 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-21T21:06:04,251 creating build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-21T21:06:04,253 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-21T21:06:04,258 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-21T21:06:04,263 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-21T21:06:04,268 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-21T21:06:04,272 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-21T21:06:04,276 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-21T21:06:04,281 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-21T21:06:04,284 running egg_info 2024-03-21T21:06:04,354 writing src/uncalled4.egg-info/PKG-INFO 2024-03-21T21:06:04,358 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2024-03-21T21:06:04,360 writing entry points to src/uncalled4.egg-info/entry_points.txt 2024-03-21T21:06:04,366 writing requirements to src/uncalled4.egg-info/requires.txt 2024-03-21T21:06:04,368 writing top-level names to src/uncalled4.egg-info/top_level.txt 2024-03-21T21:06:04,407 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-21T21:06:06,552 reading manifest template 'MANIFEST.in' 2024-03-21T21:06:06,657 adding license file 'LICENSE' 2024-03-21T21:06:06,670 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-21T21:06:06,678 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2024-03-21T21:06:06,678 !! 2024-03-21T21:06:06,679 ******************************************************************************** 2024-03-21T21:06:06,679 ############################ 2024-03-21T21:06:06,679 # Package would be ignored # 2024-03-21T21:06:06,679 ############################ 2024-03-21T21:06:06,679 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2024-03-21T21:06:06,680 but it is absent from setuptools' `packages` configuration. 2024-03-21T21:06:06,680 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T21:06:06,680 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2024-03-21T21:06:06,680 to the `packages` configuration field. 2024-03-21T21:06:06,681 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T21:06:06,681 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T21:06:06,681 instead of `find_packages(...)`/`find:`). 2024-03-21T21:06:06,681 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T21:06:06,682 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T21:06:06,682 If you don't want 'uncalled4.__pycache__' to be distributed and are 2024-03-21T21:06:06,682 already explicitly excluding 'uncalled4.__pycache__' via 2024-03-21T21:06:06,683 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T21:06:06,683 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T21:06:06,683 combination with a more fine grained `package-data` configuration. 2024-03-21T21:06:06,683 You can read more about "package data files" on setuptools documentation page: 2024-03-21T21:06:06,684 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T21:06:06,684 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T21:06:06,684 even if it does not contain any `.py` files. 2024-03-21T21:06:06,684 On the other hand, currently there is no concept of package data 2024-03-21T21:06:06,685 directory, all directories are treated like packages. 2024-03-21T21:06:06,685 ******************************************************************************** 2024-03-21T21:06:06,685 !! 2024-03-21T21:06:06,685 check.warn(importable) 2024-03-21T21:06:06,686 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2024-03-21T21:06:06,686 !! 2024-03-21T21:06:06,686 ******************************************************************************** 2024-03-21T21:06:06,686 ############################ 2024-03-21T21:06:06,687 # Package would be ignored # 2024-03-21T21:06:06,687 ############################ 2024-03-21T21:06:06,687 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2024-03-21T21:06:06,687 but it is absent from setuptools' `packages` configuration. 2024-03-21T21:06:06,687 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T21:06:06,688 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2024-03-21T21:06:06,688 to the `packages` configuration field. 2024-03-21T21:06:06,688 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T21:06:06,688 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T21:06:06,688 instead of `find_packages(...)`/`find:`). 2024-03-21T21:06:06,689 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T21:06:06,689 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T21:06:06,690 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2024-03-21T21:06:06,690 already explicitly excluding 'uncalled4.io.__pycache__' via 2024-03-21T21:06:06,690 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T21:06:06,690 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T21:06:06,690 combination with a more fine grained `package-data` configuration. 2024-03-21T21:06:06,691 You can read more about "package data files" on setuptools documentation page: 2024-03-21T21:06:06,691 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T21:06:06,691 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T21:06:06,692 even if it does not contain any `.py` files. 2024-03-21T21:06:06,692 On the other hand, currently there is no concept of package data 2024-03-21T21:06:06,692 directory, all directories are treated like packages. 2024-03-21T21:06:06,692 ******************************************************************************** 2024-03-21T21:06:06,692 !! 2024-03-21T21:06:06,693 check.warn(importable) 2024-03-21T21:06:06,693 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2024-03-21T21:06:06,693 !! 2024-03-21T21:06:06,693 ******************************************************************************** 2024-03-21T21:06:06,694 ############################ 2024-03-21T21:06:06,694 # Package would be ignored # 2024-03-21T21:06:06,694 ############################ 2024-03-21T21:06:06,694 Python recognizes 'uncalled4.models' as an importable package[^1], 2024-03-21T21:06:06,694 but it is absent from setuptools' `packages` configuration. 2024-03-21T21:06:06,695 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T21:06:06,695 package, please make sure that 'uncalled4.models' is explicitly added 2024-03-21T21:06:06,695 to the `packages` configuration field. 2024-03-21T21:06:06,695 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T21:06:06,695 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T21:06:06,696 instead of `find_packages(...)`/`find:`). 2024-03-21T21:06:06,696 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T21:06:06,696 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T21:06:06,697 If you don't want 'uncalled4.models' to be distributed and are 2024-03-21T21:06:06,697 already explicitly excluding 'uncalled4.models' via 2024-03-21T21:06:06,697 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T21:06:06,697 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T21:06:06,697 combination with a more fine grained `package-data` configuration. 2024-03-21T21:06:06,698 You can read more about "package data files" on setuptools documentation page: 2024-03-21T21:06:06,698 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T21:06:06,699 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T21:06:06,699 even if it does not contain any `.py` files. 2024-03-21T21:06:06,699 On the other hand, currently there is no concept of package data 2024-03-21T21:06:06,699 directory, all directories are treated like packages. 2024-03-21T21:06:06,699 ******************************************************************************** 2024-03-21T21:06:06,700 !! 2024-03-21T21:06:06,700 check.warn(importable) 2024-03-21T21:06:06,700 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2024-03-21T21:06:06,700 !! 2024-03-21T21:06:06,701 ******************************************************************************** 2024-03-21T21:06:06,701 ############################ 2024-03-21T21:06:06,701 # Package would be ignored # 2024-03-21T21:06:06,701 ############################ 2024-03-21T21:06:06,701 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2024-03-21T21:06:06,702 but it is absent from setuptools' `packages` configuration. 2024-03-21T21:06:06,702 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T21:06:06,702 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2024-03-21T21:06:06,702 to the `packages` configuration field. 2024-03-21T21:06:06,703 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T21:06:06,703 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T21:06:06,703 instead of `find_packages(...)`/`find:`). 2024-03-21T21:06:06,703 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T21:06:06,704 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T21:06:06,704 If you don't want 'uncalled4.models.tombo' to be distributed and are 2024-03-21T21:06:06,704 already explicitly excluding 'uncalled4.models.tombo' via 2024-03-21T21:06:06,704 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T21:06:06,705 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T21:06:06,705 combination with a more fine grained `package-data` configuration. 2024-03-21T21:06:06,705 You can read more about "package data files" on setuptools documentation page: 2024-03-21T21:06:06,706 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T21:06:06,706 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T21:06:06,706 even if it does not contain any `.py` files. 2024-03-21T21:06:06,706 On the other hand, currently there is no concept of package data 2024-03-21T21:06:06,707 directory, all directories are treated like packages. 2024-03-21T21:06:06,707 ******************************************************************************** 2024-03-21T21:06:06,707 !! 2024-03-21T21:06:06,707 check.warn(importable) 2024-03-21T21:06:06,708 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2024-03-21T21:06:06,708 !! 2024-03-21T21:06:06,708 ******************************************************************************** 2024-03-21T21:06:06,708 ############################ 2024-03-21T21:06:06,709 # Package would be ignored # 2024-03-21T21:06:06,709 ############################ 2024-03-21T21:06:06,709 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2024-03-21T21:06:06,709 but it is absent from setuptools' `packages` configuration. 2024-03-21T21:06:06,709 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T21:06:06,710 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2024-03-21T21:06:06,710 to the `packages` configuration field. 2024-03-21T21:06:06,710 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T21:06:06,711 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T21:06:06,711 instead of `find_packages(...)`/`find:`). 2024-03-21T21:06:06,711 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T21:06:06,712 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T21:06:06,712 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2024-03-21T21:06:06,712 already explicitly excluding 'uncalled4.stats.__pycache__' via 2024-03-21T21:06:06,712 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T21:06:06,713 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T21:06:06,713 combination with a more fine grained `package-data` configuration. 2024-03-21T21:06:06,713 You can read more about "package data files" on setuptools documentation page: 2024-03-21T21:06:06,713 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T21:06:06,714 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T21:06:06,714 even if it does not contain any `.py` files. 2024-03-21T21:06:06,714 On the other hand, currently there is no concept of package data 2024-03-21T21:06:06,714 directory, all directories are treated like packages. 2024-03-21T21:06:06,715 ******************************************************************************** 2024-03-21T21:06:06,715 !! 2024-03-21T21:06:06,715 check.warn(importable) 2024-03-21T21:06:06,715 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2024-03-21T21:06:06,715 !! 2024-03-21T21:06:06,715 ******************************************************************************** 2024-03-21T21:06:06,715 ############################ 2024-03-21T21:06:06,716 # Package would be ignored # 2024-03-21T21:06:06,716 ############################ 2024-03-21T21:06:06,716 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2024-03-21T21:06:06,716 but it is absent from setuptools' `packages` configuration. 2024-03-21T21:06:06,716 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T21:06:06,716 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2024-03-21T21:06:06,716 to the `packages` configuration field. 2024-03-21T21:06:06,717 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T21:06:06,717 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T21:06:06,717 instead of `find_packages(...)`/`find:`). 2024-03-21T21:06:06,717 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T21:06:06,717 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T21:06:06,718 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2024-03-21T21:06:06,718 already explicitly excluding 'uncalled4.vis.__pycache__' via 2024-03-21T21:06:06,718 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T21:06:06,718 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T21:06:06,718 combination with a more fine grained `package-data` configuration. 2024-03-21T21:06:06,718 You can read more about "package data files" on setuptools documentation page: 2024-03-21T21:06:06,719 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T21:06:06,719 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T21:06:06,719 even if it does not contain any `.py` files. 2024-03-21T21:06:06,719 On the other hand, currently there is no concept of package data 2024-03-21T21:06:06,720 directory, all directories are treated like packages. 2024-03-21T21:06:06,720 ******************************************************************************** 2024-03-21T21:06:06,720 !! 2024-03-21T21:06:06,720 check.warn(importable) 2024-03-21T21:06:06,720 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2024-03-21T21:06:06,720 !! 2024-03-21T21:06:06,721 ******************************************************************************** 2024-03-21T21:06:06,721 ############################ 2024-03-21T21:06:06,721 # Package would be ignored # 2024-03-21T21:06:06,721 ############################ 2024-03-21T21:06:06,721 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2024-03-21T21:06:06,721 but it is absent from setuptools' `packages` configuration. 2024-03-21T21:06:06,721 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T21:06:06,722 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2024-03-21T21:06:06,722 to the `packages` configuration field. 2024-03-21T21:06:06,722 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T21:06:06,722 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T21:06:06,722 instead of `find_packages(...)`/`find:`). 2024-03-21T21:06:06,722 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T21:06:06,723 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T21:06:06,723 If you don't want 'uncalled4.vis.assets' to be distributed and are 2024-03-21T21:06:06,723 already explicitly excluding 'uncalled4.vis.assets' via 2024-03-21T21:06:06,723 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T21:06:06,723 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T21:06:06,724 combination with a more fine grained `package-data` configuration. 2024-03-21T21:06:06,724 You can read more about "package data files" on setuptools documentation page: 2024-03-21T21:06:06,724 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T21:06:06,724 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T21:06:06,725 even if it does not contain any `.py` files. 2024-03-21T21:06:06,725 On the other hand, currently there is no concept of package data 2024-03-21T21:06:06,725 directory, all directories are treated like packages. 2024-03-21T21:06:06,725 ******************************************************************************** 2024-03-21T21:06:06,725 !! 2024-03-21T21:06:06,725 check.warn(importable) 2024-03-21T21:06:06,725 creating build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,725 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,726 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,726 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,726 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,726 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,726 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,726 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,728 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,731 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,734 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,737 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,741 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,744 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,747 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,750 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,753 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,756 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,758 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,762 copying src/uncalled4/__pycache__/train.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-21T21:06:06,764 creating build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-21T21:06:06,765 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-21T21:06:06,768 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-21T21:06:06,924 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-21T21:06:06,928 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-21T21:06:06,933 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-21T21:06:06,937 creating build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-21T21:06:06,939 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-21T21:06:06,943 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-21T21:06:06,946 creating build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,947 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,950 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,952 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,955 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,958 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,960 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,963 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,966 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,968 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,971 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,973 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,975 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,978 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,980 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-21T21:06:06,983 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:06,983 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:06,986 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:06,988 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:06,990 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:06,993 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:06,996 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,000 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,002 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,005 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,008 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,011 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,014 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,017 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,020 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,023 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-21T21:06:07,025 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-21T21:06:07,026 copying src/uncalled4/vis/assets/.browser.js.swp -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-21T21:06:07,030 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-21T21:06:07,032 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-21T21:06:07,035 creating build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,036 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,039 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,042 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,045 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,047 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,050 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,052 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,055 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,058 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,061 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-21T21:06:07,067 running build_ext 2024-03-21T21:06:07,792 building '_uncalled4' extension 2024-03-21T21:06:08,654 creating build/temp.linux-armv7l-cpython-39 2024-03-21T21:06:08,656 creating build/temp.linux-armv7l-cpython-39/src 2024-03-21T21:06:08,952 creating build/temp.linux-armv7l-cpython-39/src/cpp 2024-03-21T21:06:09,176 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/config.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/config.o -std=c++11 -O3 -g 2024-03-21T21:06:15,500 In file included from src/cpp/dtw.hpp:7, 2024-03-21T21:06:15,501 from src/cpp/config.hpp:30, 2024-03-21T21:06:15,501 from src/cpp/config.cpp:1: 2024-03-21T21:06:15,501 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:15,502 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T21:06:15,502 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:15,502 192 | struct PyArray { 2024-03-21T21:06:15,502 | ^~~~~~~ 2024-03-21T21:06:15,688 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:15,689 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-21T21:06:15,689 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:15,772 In file included from src/cpp/aln.hpp:11, 2024-03-21T21:06:15,772 from src/cpp/dtw.hpp:9, 2024-03-21T21:06:15,772 from src/cpp/config.hpp:30, 2024-03-21T21:06:15,772 from src/cpp/config.cpp:1: 2024-03-21T21:06:15,772 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-21T21:06:15,773 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:06:15,773 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-21T21:06:15,773 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-21T21:06:15,774 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:06:15,774 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-21T21:06:15,815 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-21T21:06:15,815 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] 2024-03-21T21:06:15,816 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-21T21:06:15,816 | ~~^~~~~~~~~~ 2024-03-21T21:06:15,817 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-21T21:06:15,817 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] 2024-03-21T21:06:15,817 158 | normalize({0, events.size(), scale, shift}); 2024-03-21T21:06:15,817 | ~~~~~~~~~~~^~ 2024-03-21T21:06:15,860 In file included from src/cpp/dtw.hpp:7, 2024-03-21T21:06:15,860 from src/cpp/config.hpp:30, 2024-03-21T21:06:15,860 from src/cpp/config.cpp:1: 2024-03-21T21:06:15,860 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:15,860 src/cpp/event_detector.hpp:211:39: required from here 2024-03-21T21:06:15,861 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:15,861 192 | struct PyArray { 2024-03-21T21:06:15,861 | ^~~~~~~ 2024-03-21T21:06:15,953 In file included from src/cpp/dtw.hpp:9, 2024-03-21T21:06:15,954 from src/cpp/config.hpp:30, 2024-03-21T21:06:15,954 from src/cpp/config.cpp:1: 2024-03-21T21:06:15,954 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-21T21:06:15,954 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-21T21:06:15,954 187 | i64 ref; 2024-03-21T21:06:15,954 | ^~~ 2024-03-21T21:06:15,959 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-21T21:06:15,959 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-21T21:06:15,959 279 | int len,dist; 2024-03-21T21:06:15,959 | ^~~~ 2024-03-21T21:06:15,970 In file included from src/cpp/dtw.hpp:7, 2024-03-21T21:06:15,970 from src/cpp/config.hpp:30, 2024-03-21T21:06:15,970 from src/cpp/config.cpp:1: 2024-03-21T21:06:15,970 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:15,971 src/cpp/aln.hpp:383:23: required from here 2024-03-21T21:06:15,971 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:15,971 192 | struct PyArray { 2024-03-21T21:06:15,971 | ^~~~~~~ 2024-03-21T21:06:16,064 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:16,064 src/cpp/dtw.hpp:395:26: required from here 2024-03-21T21:06:16,064 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:32,499 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/dtw.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/dtw.o -std=c++11 -O3 -g 2024-03-21T21:06:37,301 In file included from src/cpp/dtw.hpp:7, 2024-03-21T21:06:37,302 from src/cpp/dtw.cpp:1: 2024-03-21T21:06:37,302 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:37,302 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T21:06:37,302 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:37,302 192 | struct PyArray { 2024-03-21T21:06:37,302 | ^~~~~~~ 2024-03-21T21:06:37,489 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:37,489 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-21T21:06:37,489 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:37,572 In file included from src/cpp/aln.hpp:11, 2024-03-21T21:06:37,573 from src/cpp/dtw.hpp:9, 2024-03-21T21:06:37,573 from src/cpp/dtw.cpp:1: 2024-03-21T21:06:37,573 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-21T21:06:37,573 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:06:37,573 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-21T21:06:37,573 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-21T21:06:37,574 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:06:37,574 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-21T21:06:37,615 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-21T21:06:37,615 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] 2024-03-21T21:06:37,616 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-21T21:06:37,616 | ~~^~~~~~~~~~ 2024-03-21T21:06:37,616 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-21T21:06:37,616 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] 2024-03-21T21:06:37,616 158 | normalize({0, events.size(), scale, shift}); 2024-03-21T21:06:37,617 | ~~~~~~~~~~~^~ 2024-03-21T21:06:37,659 In file included from src/cpp/dtw.hpp:7, 2024-03-21T21:06:37,659 from src/cpp/dtw.cpp:1: 2024-03-21T21:06:37,659 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:37,660 src/cpp/event_detector.hpp:211:39: required from here 2024-03-21T21:06:37,660 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:37,660 192 | struct PyArray { 2024-03-21T21:06:37,660 | ^~~~~~~ 2024-03-21T21:06:37,753 In file included from src/cpp/dtw.hpp:9, 2024-03-21T21:06:37,753 from src/cpp/dtw.cpp:1: 2024-03-21T21:06:37,753 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-21T21:06:37,753 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-21T21:06:37,753 187 | i64 ref; 2024-03-21T21:06:37,754 | ^~~ 2024-03-21T21:06:37,757 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-21T21:06:37,757 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-21T21:06:37,757 279 | int len,dist; 2024-03-21T21:06:37,758 | ^~~~ 2024-03-21T21:06:37,768 In file included from src/cpp/dtw.hpp:7, 2024-03-21T21:06:37,768 from src/cpp/dtw.cpp:1: 2024-03-21T21:06:37,768 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:37,768 src/cpp/aln.hpp:383:23: required from here 2024-03-21T21:06:37,768 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:37,769 192 | struct PyArray { 2024-03-21T21:06:37,769 | ^~~~~~~ 2024-03-21T21:06:37,861 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:37,862 src/cpp/dtw.hpp:395:26: required from here 2024-03-21T21:06:37,862 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:37,881 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2024-03-21T21:06:37,881 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2024-03-21T21:06:37,881 21 | size_t i = 0, j = 0, b = 0; 2024-03-21T21:06:37,881 | ^ 2024-03-21T21:06:37,885 In file included from src/cpp/dtw.hpp:7, 2024-03-21T21:06:37,886 from src/cpp/dtw.cpp:1: 2024-03-21T21:06:37,886 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:06:37,886 src/cpp/dtw.cpp:64:30: required from here 2024-03-21T21:06:37,886 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:06:37,886 192 | struct PyArray { 2024-03-21T21:06:37,887 | ^~~~~~~ 2024-03-21T21:06:37,892 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2024-03-21T21:06:37,893 src/cpp/dtw.cpp:98:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2024-03-21T21:06:37,893 98 | auto fill = backfill_na ? samps : Interval(); 2024-03-21T21:06:37,893 | ^~~~ 2024-03-21T21:07:33,533 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/event_detector.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/event_detector.o -std=c++11 -O3 -g 2024-03-21T21:07:38,393 In file included from src/cpp/intervals.hpp:11, 2024-03-21T21:07:38,393 from src/cpp/event_detector.hpp:13, 2024-03-21T21:07:38,394 from src/cpp/event_detector.cpp:15: 2024-03-21T21:07:38,394 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:07:38,394 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T21:07:38,394 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:07:38,394 192 | struct PyArray { 2024-03-21T21:07:38,394 | ^~~~~~~ 2024-03-21T21:07:38,414 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:07:38,414 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-21T21:07:38,414 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:07:38,501 In file included from src/cpp/event_detector.cpp:15: 2024-03-21T21:07:38,502 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-21T21:07:38,502 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:07:38,502 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-21T21:07:38,502 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-21T21:07:38,502 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:07:38,503 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-21T21:07:38,533 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-21T21:07:38,533 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] 2024-03-21T21:07:38,533 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-21T21:07:38,534 | ~~^~~~~~~~~~ 2024-03-21T21:07:38,534 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-21T21:07:38,534 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] 2024-03-21T21:07:38,534 158 | normalize({0, events.size(), scale, shift}); 2024-03-21T21:07:38,534 | ~~~~~~~~~~~^~ 2024-03-21T21:07:38,577 In file included from src/cpp/intervals.hpp:11, 2024-03-21T21:07:38,577 from src/cpp/event_detector.hpp:13, 2024-03-21T21:07:38,578 from src/cpp/event_detector.cpp:15: 2024-03-21T21:07:38,578 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:07:38,578 src/cpp/event_detector.hpp:211:39: required from here 2024-03-21T21:07:38,578 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:07:38,578 192 | struct PyArray { 2024-03-21T21:07:38,578 | ^~~~~~~ 2024-03-21T21:07:38,632 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:07:38,633 src/cpp/event_detector.cpp:242:30: required from here 2024-03-21T21:07:38,633 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:08:02,361 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/intervals.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/intervals.o -std=c++11 -O3 -g 2024-03-21T21:08:07,151 In file included from src/cpp/intervals.hpp:11, 2024-03-21T21:08:07,151 from src/cpp/intervals.cpp:2: 2024-03-21T21:08:07,151 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:08:07,151 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T21:08:07,151 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:08:07,152 192 | struct PyArray { 2024-03-21T21:08:07,152 | ^~~~~~~ 2024-03-21T21:08:09,141 In file included from src/cpp/intervals.cpp:2: 2024-03-21T21:08:09,142 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2024-03-21T21:08:09,142 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]’ 2024-03-21T21:08:09,142 src/cpp/intervals.cpp:7:25: required from here 2024-03-21T21:08:09,142 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] 2024-03-21T21:08:09,142 348 | while (gap >= MAX_LEN_I16) { 2024-03-21T21:08:09,143 | ~~~~^~~~~~~~~~~~~~ 2024-03-21T21:08:39,899 In file included from /usr/include/c++/10/vector:72, 2024-03-21T21:08:39,900 from src/cpp/intervals.hpp:6, 2024-03-21T21:08:39,900 from src/cpp/intervals.cpp:2: 2024-03-21T21:08:39,900 /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 >]’: 2024-03-21T21:08:39,900 /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 2024-03-21T21:08:39,900 426 | vector<_Tp, _Alloc>:: 2024-03-21T21:08:39,901 | ^~~~~~~~~~~~~~~~~~~ 2024-03-21T21:08:39,982 In file included from /usr/include/c++/10/vector:67, 2024-03-21T21:08:39,982 from src/cpp/intervals.hpp:6, 2024-03-21T21:08:39,982 from src/cpp/intervals.cpp:2: 2024-03-21T21:08:39,982 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::mirror() const [with T = long long int]’: 2024-03-21T21:08:39,983 /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 2024-03-21T21:08:39,983 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:39,983 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:08:40,049 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’: 2024-03-21T21:08:40,049 /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 2024-03-21T21:08:40,049 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:40,050 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:08:40,050 /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 2024-03-21T21:08:40,050 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:40,050 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:08:40,152 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::intersect(IntervalIndex) const [with T = long long int]’: 2024-03-21T21:08:40,152 /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 2024-03-21T21:08:40,152 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:40,153 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:08:40,248 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’: 2024-03-21T21:08:40,248 /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 2024-03-21T21:08:40,249 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:40,249 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:08:40,249 /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 2024-03-21T21:08:40,249 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:40,249 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:08:40,249 /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 2024-03-21T21:08:40,250 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:40,250 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:08:50,344 In file included from /usr/include/c++/10/vector:72, 2024-03-21T21:08:50,344 from src/cpp/intervals.hpp:6, 2024-03-21T21:08:50,344 from src/cpp/intervals.cpp:2: 2024-03-21T21:08:50,344 /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 >]’: 2024-03-21T21:08:50,344 /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 2024-03-21T21:08:50,345 426 | vector<_Tp, _Alloc>:: 2024-03-21T21:08:50,345 | ^~~~~~~~~~~~~~~~~~~ 2024-03-21T21:08:50,415 /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]’: 2024-03-21T21:08:50,415 /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 2024-03-21T21:08:50,416 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-03-21T21:08:50,416 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-21T21:08:50,612 In file included from /usr/include/c++/10/vector:67, 2024-03-21T21:08:50,613 from src/cpp/intervals.hpp:6, 2024-03-21T21:08:50,613 from src/cpp/intervals.cpp:2: 2024-03-21T21:08:50,613 /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&)’: 2024-03-21T21:08:50,613 /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 2024-03-21T21:08:50,613 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:50,613 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:08:50,614 /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 2024-03-21T21:08:50,614 1198 | _M_realloc_insert(end(), __x); 2024-03-21T21:08:50,614 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T21:09:00,508 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/normalizer.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/normalizer.o -std=c++11 -O3 -g 2024-03-21T21:09:10,776 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/pore_model.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/pore_model.o -std=c++11 -O3 -g 2024-03-21T21:09:15,546 In file included from src/cpp/pore_model.hpp:36, 2024-03-21T21:09:15,546 from src/cpp/pore_model.cpp:1: 2024-03-21T21:09:15,546 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:15,546 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T21:09:15,546 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:15,547 192 | struct PyArray { 2024-03-21T21:09:15,547 | ^~~~~~~ 2024-03-21T21:09:48,113 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.9 -c src/cpp/pybinder.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/pybinder.o -std=c++11 -O3 -g 2024-03-21T21:09:52,916 In file included from src/cpp/read_buffer.hpp:30, 2024-03-21T21:09:52,916 from src/cpp/pybinder.cpp:5: 2024-03-21T21:09:52,916 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:52,916 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-21T21:09:52,917 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:52,917 192 | struct PyArray { 2024-03-21T21:09:52,917 | ^~~~~~~ 2024-03-21T21:09:52,944 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:52,944 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T21:09:52,945 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:53,031 In file included from src/cpp/signal_processor.hpp:7, 2024-03-21T21:09:53,031 from src/cpp/pybinder.cpp:6: 2024-03-21T21:09:53,031 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-21T21:09:53,031 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:09:53,031 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-21T21:09:53,032 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-21T21:09:53,032 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:09:53,032 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-21T21:09:53,062 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-21T21:09:53,062 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] 2024-03-21T21:09:53,062 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-21T21:09:53,063 | ~~^~~~~~~~~~ 2024-03-21T21:09:53,063 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-21T21:09:53,063 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] 2024-03-21T21:09:53,063 158 | normalize({0, events.size(), scale, shift}); 2024-03-21T21:09:53,063 | ~~~~~~~~~~~^~ 2024-03-21T21:09:53,106 In file included from src/cpp/read_buffer.hpp:30, 2024-03-21T21:09:53,106 from src/cpp/pybinder.cpp:5: 2024-03-21T21:09:53,106 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:53,106 src/cpp/event_detector.hpp:211:39: required from here 2024-03-21T21:09:53,107 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:53,107 192 | struct PyArray { 2024-03-21T21:09:53,107 | ^~~~~~~ 2024-03-21T21:09:53,372 In file included from src/cpp/dtw.hpp:9, 2024-03-21T21:09:53,373 from src/cpp/pybinder.cpp:8: 2024-03-21T21:09:53,373 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-21T21:09:53,373 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-21T21:09:53,373 187 | i64 ref; 2024-03-21T21:09:53,373 | ^~~ 2024-03-21T21:09:53,377 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-21T21:09:53,377 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-21T21:09:53,377 279 | int len,dist; 2024-03-21T21:09:53,377 | ^~~~ 2024-03-21T21:09:53,387 In file included from src/cpp/read_buffer.hpp:30, 2024-03-21T21:09:53,388 from src/cpp/pybinder.cpp:5: 2024-03-21T21:09:53,388 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:53,388 src/cpp/aln.hpp:383:23: required from here 2024-03-21T21:09:53,388 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:53,388 192 | struct PyArray { 2024-03-21T21:09:53,388 | ^~~~~~~ 2024-03-21T21:09:53,480 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:53,480 src/cpp/dtw.hpp:395:26: required from here 2024-03-21T21:09:53,481 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:53,518 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:53,518 src/cpp/eventalign.hpp:110:31: required from here 2024-03-21T21:09:53,518 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:56,906 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:56,906 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const string&, pybind11::array_t, bool, pybind11::array_t, pybind11::array_t, pybind11::array_t, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string; typename ModelType::kmer_t = short unsigned int]’ 2024-03-21T21:09:56,907 src/cpp/pybinder.cpp:31:10: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T21:09:56,907 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:09:56,907 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:56,933 In file included from src/cpp/pybinder.cpp:10: 2024-03-21T21:09:56,934 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]’: 2024-03-21T21:09:56,934 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]’ 2024-03-21T21:09:56,934 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:09:56,934 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:09:56,934 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-21T21:09:56,934 | ~~^~~~~~~~~~~ 2024-03-21T21:09:57,089 In file included from src/cpp/read_buffer.hpp:30, 2024-03-21T21:09:57,089 from src/cpp/pybinder.cpp:5: 2024-03-21T21:09:57,090 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T21:09:57,090 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const string&, pybind11::array_t, bool, pybind11::array_t, pybind11::array_t, pybind11::array_t, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string; typename ModelType::kmer_t = unsigned int]’ 2024-03-21T21:09:57,090 src/cpp/pybinder.cpp:31:10: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T21:09:57,090 src/cpp/pybinder.cpp:67:31: required from here 2024-03-21T21:09:57,090 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T21:09:57,090 192 | struct PyArray { 2024-03-21T21:09:57,091 | ^~~~~~~ 2024-03-21T21:09:57,113 In file included from src/cpp/pybinder.cpp:10: 2024-03-21T21:09:57,113 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]’: 2024-03-21T21:09:57,114 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]’ 2024-03-21T21:09:57,114 src/cpp/pybinder.cpp:67:31: required from here 2024-03-21T21:09:57,114 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T21:09:57,114 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-21T21:09:57,114 | ~~^~~~~~~~~~~ 2024-03-21T21:10:03,537 In file included from src/cpp/pybinder.cpp:8: 2024-03-21T21:10:03,537 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-21T21:10:03,537 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]’ 2024-03-21T21:10:03,537 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]’ 2024-03-21T21:10:03,537 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:10:03,538 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-21T21:10:03,538 644 | if (q0 >= qry_size()) { 2024-03-21T21:10:03,538 | ~~~^~~~~~~~~~~~~ 2024-03-21T21:10:03,538 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-21T21:10:03,538 651 | if (r1 > ref_size()) { 2024-03-21T21:10:03,538 | ~~~^~~~~~~~~~~~ 2024-03-21T21:10:04,090 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-21T21:10:04,090 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]’ 2024-03-21T21:10:04,091 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]’ 2024-03-21T21:10:04,091 src/cpp/pybinder.cpp:67:31: required from here 2024-03-21T21:10:04,091 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-21T21:10:04,091 644 | if (q0 >= qry_size()) { 2024-03-21T21:10:04,091 | ~~~^~~~~~~~~~~~~ 2024-03-21T21:10:04,091 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-21T21:10:04,092 651 | if (r1 > ref_size()) { 2024-03-21T21:10:04,092 | ~~~^~~~~~~~~~~~ 2024-03-21T21:10:14,471 In file included from src/cpp/seq.hpp:32, 2024-03-21T21:10:14,471 from src/cpp/pybinder.cpp:7: 2024-03-21T21:10:14,472 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]’: 2024-03-21T21:10:14,472 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]’ 2024-03-21T21:10:14,472 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]’ 2024-03-21T21:10:14,472 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]’ 2024-03-21T21:10:14,472 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]’ 2024-03-21T21:10:14,473 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:10:14,473 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-21T21:10:14,473 507 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2024-03-21T21:10:14,473 | ~~~~~~~~~~^ 2024-03-21T21:10:14,473 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]’: 2024-03-21T21:10:14,473 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]’ 2024-03-21T21:10:14,474 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]’ 2024-03-21T21:10:14,474 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]’ 2024-03-21T21:10:14,474 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]’ 2024-03-21T21:10:14,474 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:10:14,474 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-21T21:10:18,919 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]’: 2024-03-21T21:10:18,919 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]’ 2024-03-21T21:10:18,919 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]’ 2024-03-21T21:10:18,920 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]’ 2024-03-21T21:10:18,920 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]’ 2024-03-21T21:10:18,920 src/cpp/pybinder.cpp:67:31: required from here 2024-03-21T21:10:18,920 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-21T21:10:18,920 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]’: 2024-03-21T21:10:18,920 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]’ 2024-03-21T21:10:18,921 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]’ 2024-03-21T21:10:18,921 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]’ 2024-03-21T21:10:18,921 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]’ 2024-03-21T21:10:18,921 src/cpp/pybinder.cpp:67:31: required from here 2024-03-21T21:10:18,921 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-21T21:10:23,431 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]’: 2024-03-21T21:10:23,431 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-21T21:10:23,431 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-21T21:10:23,432 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-21T21:10:23,432 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-21T21:10:23,432 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]’ 2024-03-21T21:10:23,432 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]’ 2024-03-21T21:10:23,432 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:10:23,432 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-21T21:10:23,433 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-21T21:10:23,433 | ^~~~~~~~ 2024-03-21T21:10:24,161 In file included from src/cpp/pybinder.cpp:8: 2024-03-21T21:10:24,161 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-21T21:10:24,161 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]’ 2024-03-21T21:10:24,162 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-21T21:10:24,162 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-21T21:10:24,162 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-21T21:10:24,162 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]’ 2024-03-21T21:10:24,162 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T21:10:24,162 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:10:24,163 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] 2024-03-21T21:10:24,163 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-21T21:10:24,163 | ~~^~~~~~~~~~~~ 2024-03-21T21:10:24,164 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-21T21:10:24,164 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]’ 2024-03-21T21:10:24,165 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-21T21:10:24,165 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-21T21:10:24,165 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-21T21:10:24,165 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]’ 2024-03-21T21:10:24,165 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]’ 2024-03-21T21:10:24,165 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:10:24,165 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] 2024-03-21T21:10:24,166 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-21T21:10:24,166 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-21T21:10:25,021 In file included from src/cpp/seq.hpp:32, 2024-03-21T21:10:25,021 from src/cpp/pybinder.cpp:7: 2024-03-21T21:10:25,021 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]’: 2024-03-21T21:10:25,021 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2024-03-21T21:10:25,021 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-21T21:10:25,022 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-21T21:10:25,022 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-21T21:10:25,022 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]’ 2024-03-21T21:10:25,022 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]’ 2024-03-21T21:10:25,022 src/cpp/pybinder.cpp:67:31: required from here 2024-03-21T21:10:25,022 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-21T21:10:25,023 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-21T21:10:25,023 | ^~~~~~~~ 2024-03-21T21:10:25,183 In file included from src/cpp/pybinder.cpp:8: 2024-03-21T21:10:25,183 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-21T21:10:25,183 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]’ 2024-03-21T21:10:25,183 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-21T21:10:25,184 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-21T21:10:25,184 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-21T21:10:25,184 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]’ 2024-03-21T21:10:25,184 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]’ 2024-03-21T21:10:25,184 src/cpp/pybinder.cpp:67:31: required from here 2024-03-21T21:10:25,184 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] 2024-03-21T21:10:25,184 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-21T21:10:25,185 | ~~^~~~~~~~~~~~ 2024-03-21T21:10:25,186 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-21T21:10:25,186 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]’ 2024-03-21T21:10:25,186 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-21T21:10:25,187 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-21T21:10:25,187 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-21T21:10:25,187 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]’ 2024-03-21T21:10:25,187 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]’ 2024-03-21T21:10:25,187 src/cpp/pybinder.cpp:67:31: required from here 2024-03-21T21:10:25,187 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] 2024-03-21T21:10:25,187 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-21T21:10:25,188 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-21T21:10:26,653 In file included from src/cpp/read_buffer.hpp:30, 2024-03-21T21:10:26,653 from src/cpp/pybinder.cpp:5: 2024-03-21T21:10:26,653 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2024-03-21T21:10:26,654 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]’ 2024-03-21T21:10:26,654 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-21T21:10:26,654 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-21T21:10:26,654 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-21T21:10:26,654 /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/.eggs/pybind11-2.11.1-py3.9.egg/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-21T21:10:26,654 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]’ 2024-03-21T21:10:26,655 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]’ 2024-03-21T21:10:26,655 src/cpp/pybinder.cpp:66:31: required from here 2024-03-21T21:10:26,655 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2024-03-21T21:10:26,655 144 | auto sum = super::sum(); 2024-03-21T21:10:26,655 | ^~~ 2024-03-21T21:10:26,655 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2024-03-21T21:10:26,655 145 | auto len = super::size(); 2024-03-21T21:10:26,656 | ^~~ 2024-03-21T21:10:42,293 virtual memory exhausted: Cannot allocate memory 2024-03-21T21:10:42,411 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-03-21T21:10:42,543 ERROR: python setup.py bdist_wheel exited with 1 2024-03-21T21:10:42,560 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2024-03-21T21:10:42,560 exec(compile('"'"''"'"''"'"' 2024-03-21T21:10:42,560 # This is -- a caller that pip uses to run setup.py 2024-03-21T21:10:42,560 # 2024-03-21T21:10:42,560 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-03-21T21:10:42,560 # import from `distutils.core` to work with newer packaging standards. 2024-03-21T21:10:42,560 # - It provides a clear error message when setuptools is not installed. 2024-03-21T21:10:42,560 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-03-21T21:10:42,560 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-03-21T21:10:42,560 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-03-21T21:10:42,560 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-03-21T21:10:42,560 import os, sys, tokenize 2024-03-21T21:10:42,560 2024-03-21T21:10:42,560 try: 2024-03-21T21:10:42,560 import setuptools 2024-03-21T21:10:42,560 except ImportError as error: 2024-03-21T21:10:42,560 print( 2024-03-21T21:10:42,560 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-03-21T21:10:42,560 "the build environment.", 2024-03-21T21:10:42,560 file=sys.stderr, 2024-03-21T21:10:42,560 ) 2024-03-21T21:10:42,560 sys.exit(1) 2024-03-21T21:10:42,560 2024-03-21T21:10:42,560 __file__ = %r 2024-03-21T21:10:42,560 sys.argv[0] = __file__ 2024-03-21T21:10:42,560 2024-03-21T21:10:42,560 if os.path.exists(__file__): 2024-03-21T21:10:42,560 filename = __file__ 2024-03-21T21:10:42,560 with tokenize.open(__file__) as f: 2024-03-21T21:10:42,560 setup_py_code = f.read() 2024-03-21T21:10:42,560 else: 2024-03-21T21:10:42,560 filename = "" 2024-03-21T21:10:42,560 setup_py_code = "from setuptools import setup; setup()" 2024-03-21T21:10:42,560 2024-03-21T21:10:42,560 exec(compile(setup_py_code, filename, "exec")) 2024-03-21T21:10:42,560 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-lix5f3cg[/] 2024-03-21T21:10:42,560 [bold magenta]cwd[/]: /tmp/pip-wheel-6_elnzuc/uncalled4_59f1a8b2d4464d86bb1cdf0fcce6baac/ 2024-03-21T21:10:42,561 Building wheel for uncalled4 (setup.py): finished with status 'error' 2024-03-21T21:10:42,562 ERROR: Failed building wheel for uncalled4 2024-03-21T21:10:42,563 Running setup.py clean for uncalled4 2024-03-21T21:10:42,563 Running command python setup.py clean 2024-03-21T21:10:43,497 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-21T21:10:43,497 !! 2024-03-21T21:10:43,497 ******************************************************************************** 2024-03-21T21:10:43,498 Requirements should be satisfied by a PEP 517 installer. 2024-03-21T21:10:43,498 If you are using pip, you can try `pip install --use-pep517`. 2024-03-21T21:10:43,498 ******************************************************************************** 2024-03-21T21:10:43,498 !! 2024-03-21T21:10:43,498 dist.fetch_build_eggs(dist.setup_requires) 2024-03-21T21:10:43,690 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-21T21:10:43,690 warnings.warn(msg) 2024-03-21T21:10:43,849 running clean 2024-03-21T21:10:43,898 removing 'build/temp.linux-armv7l-cpython-39' (and everything under it) 2024-03-21T21:10:43,913 removing 'build/lib.linux-armv7l-cpython-39' (and everything under it) 2024-03-21T21:10:43,945 'build/bdist.linux-armv7l' does not exist -- can't clean it 2024-03-21T21:10:43,945 'build/scripts-3.9' does not exist -- can't clean it 2024-03-21T21:10:43,946 removing 'build' 2024-03-21T21:10:44,037 Failed to build uncalled4 2024-03-21T21:10:44,038 ERROR: Failed to build one or more wheels 2024-03-21T21:10:44,040 Exception information: 2024-03-21T21:10:44,040 Traceback (most recent call last): 2024-03-21T21:10:44,040 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2024-03-21T21:10:44,040 status = run_func(*args) 2024-03-21T21:10:44,040 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2024-03-21T21:10:44,040 return func(self, options, args) 2024-03-21T21:10:44,040 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2024-03-21T21:10:44,040 raise CommandError("Failed to build one or more wheels") 2024-03-21T21:10:44,040 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-03-21T21:10:44,043 Removed build tracker: '/tmp/pip-build-tracker-zo10dc4v'