2024-03-03T23:12:23,151 Created temporary directory: /tmp/pip-build-tracker-l5oju6vo 2024-03-03T23:12:23,152 Initialized build tracking at /tmp/pip-build-tracker-l5oju6vo 2024-03-03T23:12:23,153 Created build tracker: /tmp/pip-build-tracker-l5oju6vo 2024-03-03T23:12:23,153 Entered build tracker: /tmp/pip-build-tracker-l5oju6vo 2024-03-03T23:12:23,154 Created temporary directory: /tmp/pip-wheel-gnyb8mtt 2024-03-03T23:12:23,157 Created temporary directory: /tmp/pip-ephem-wheel-cache-9jw936_v 2024-03-03T23:12:23,179 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-03T23:12:23,182 2 location(s) to search for versions of uncalled4: 2024-03-03T23:12:23,182 * https://pypi.org/simple/uncalled4/ 2024-03-03T23:12:23,182 * https://www.piwheels.org/simple/uncalled4/ 2024-03-03T23:12:23,183 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2024-03-03T23:12:23,184 Getting page https://pypi.org/simple/uncalled4/ 2024-03-03T23:12:23,185 Found index url https://pypi.org/simple/ 2024-03-03T23:12:23,402 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2024-03-03T23:12:23,404 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 2024-03-03T23:12:23,404 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2024-03-03T23:12:23,405 Getting page https://www.piwheels.org/simple/uncalled4/ 2024-03-03T23:12:23,406 Found index url https://www.piwheels.org/simple/ 2024-03-03T23:12:23,864 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2024-03-03T23:12:23,865 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2024-03-03T23:12:23,866 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2024-03-03T23:12:23,886 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2024-03-03T23:12:23,905 Collecting uncalled4==3.5.1 2024-03-03T23:12:23,907 Created temporary directory: /tmp/pip-unpack-ewb0vh_o 2024-03-03T23:12:24,142 Downloading uncalled4-3.5.1.tar.gz (15.3 MB) 2024-03-03T23:12:30,184 Added uncalled4==3.5.1 from https://files.pythonhosted.org/packages/84/34/b2d0e57215e66cb04e9185ad6f858f3ded32b197dee61328b96d3dddd47a/uncalled4-3.5.1.tar.gz to build tracker '/tmp/pip-build-tracker-l5oju6vo' 2024-03-03T23:12:30,187 Running setup.py (path:/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/setup.py) egg_info for package uncalled4 2024-03-03T23:12:30,188 Created temporary directory: /tmp/pip-pip-egg-info-xmqmmmvs 2024-03-03T23:12:30,188 Preparing metadata (setup.py): started 2024-03-03T23:12:30,190 Running command python setup.py egg_info 2024-03-03T23:12:31,079 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-03T23:12:31,079 !! 2024-03-03T23:12:31,080 ******************************************************************************** 2024-03-03T23:12:31,081 Requirements should be satisfied by a PEP 517 installer. 2024-03-03T23:12:31,081 If you are using pip, you can try `pip install --use-pep517`. 2024-03-03T23:12:31,082 ******************************************************************************** 2024-03-03T23:12:31,083 !! 2024-03-03T23:12:31,083 dist.fetch_build_eggs(dist.setup_requires) 2024-03-03T23:12:33,949 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-03T23:12:33,950 warnings.warn(msg) 2024-03-03T23:12:34,039 running egg_info 2024-03-03T23:12:34,040 creating /tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info 2024-03-03T23:12:34,067 writing /tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info/PKG-INFO 2024-03-03T23:12:34,070 writing dependency_links to /tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info/dependency_links.txt 2024-03-03T23:12:34,071 writing entry points to /tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info/entry_points.txt 2024-03-03T23:12:34,073 writing requirements to /tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info/requires.txt 2024-03-03T23:12:34,074 writing top-level names to /tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info/top_level.txt 2024-03-03T23:12:34,075 writing manifest file '/tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info/SOURCES.txt' 2024-03-03T23:12:34,194 reading manifest file '/tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info/SOURCES.txt' 2024-03-03T23:12:34,196 reading manifest template 'MANIFEST.in' 2024-03-03T23:12:34,243 adding license file 'LICENSE' 2024-03-03T23:12:34,249 writing manifest file '/tmp/pip-pip-egg-info-xmqmmmvs/uncalled4.egg-info/SOURCES.txt' 2024-03-03T23:12:34,364 Preparing metadata (setup.py): finished with status 'done' 2024-03-03T23:12:34,368 Source in /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0 has version 3.5.1, which satisfies requirement uncalled4==3.5.1 from https://files.pythonhosted.org/packages/84/34/b2d0e57215e66cb04e9185ad6f858f3ded32b197dee61328b96d3dddd47a/uncalled4-3.5.1.tar.gz 2024-03-03T23:12:34,369 Removed uncalled4==3.5.1 from https://files.pythonhosted.org/packages/84/34/b2d0e57215e66cb04e9185ad6f858f3ded32b197dee61328b96d3dddd47a/uncalled4-3.5.1.tar.gz from build tracker '/tmp/pip-build-tracker-l5oju6vo' 2024-03-03T23:12:34,374 Created temporary directory: /tmp/pip-unpack-gj656_bh 2024-03-03T23:12:34,375 Created temporary directory: /tmp/pip-unpack-u2qkkrl0 2024-03-03T23:12:34,388 Building wheels for collected packages: uncalled4 2024-03-03T23:12:34,392 Created temporary directory: /tmp/pip-wheel-wg7ivqnv 2024-03-03T23:12:34,392 Building wheel for uncalled4 (setup.py): started 2024-03-03T23:12:34,394 Destination directory: /tmp/pip-wheel-wg7ivqnv 2024-03-03T23:12:34,394 Running command python setup.py bdist_wheel 2024-03-03T23:12:35,256 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-03T23:12:35,256 !! 2024-03-03T23:12:35,257 ******************************************************************************** 2024-03-03T23:12:35,258 Requirements should be satisfied by a PEP 517 installer. 2024-03-03T23:12:35,259 If you are using pip, you can try `pip install --use-pep517`. 2024-03-03T23:12:35,259 ******************************************************************************** 2024-03-03T23:12:35,260 !! 2024-03-03T23:12:35,261 dist.fetch_build_eggs(dist.setup_requires) 2024-03-03T23:12:35,480 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-03T23:12:35,481 warnings.warn(msg) 2024-03-03T23:12:35,653 running bdist_wheel 2024-03-03T23:12:35,784 running build 2024-03-03T23:12:35,784 running build_py 2024-03-03T23:12:35,814 creating build 2024-03-03T23:12:35,815 creating build/lib.linux-armv7l-cpython-311 2024-03-03T23:12:35,816 creating build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,817 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,820 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,822 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,825 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,827 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,829 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,832 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,835 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,838 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,840 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,842 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,845 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,848 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,850 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-03T23:12:35,852 creating build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-03T23:12:35,853 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-03T23:12:35,855 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-03T23:12:35,856 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-03T23:12:35,858 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-03T23:12:35,861 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-03T23:12:35,862 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-03T23:12:35,865 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-03T23:12:35,867 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-03T23:12:35,869 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-03T23:12:35,871 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-03T23:12:35,874 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-03T23:12:35,876 creating build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-03T23:12:35,878 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-03T23:12:35,880 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-03T23:12:35,882 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-03T23:12:35,885 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-03T23:12:35,888 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-03T23:12:35,890 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-03T23:12:35,892 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-03T23:12:35,894 running egg_info 2024-03-03T23:12:35,921 writing src/uncalled4.egg-info/PKG-INFO 2024-03-03T23:12:35,924 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2024-03-03T23:12:35,926 writing entry points to src/uncalled4.egg-info/entry_points.txt 2024-03-03T23:12:35,928 writing requirements to src/uncalled4.egg-info/requires.txt 2024-03-03T23:12:35,930 writing top-level names to src/uncalled4.egg-info/top_level.txt 2024-03-03T23:12:35,963 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-03T23:12:35,968 reading manifest template 'MANIFEST.in' 2024-03-03T23:12:36,012 adding license file 'LICENSE' 2024-03-03T23:12:36,019 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-03T23:12:36,023 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2024-03-03T23:12:36,024 !! 2024-03-03T23:12:36,025 ******************************************************************************** 2024-03-03T23:12:36,026 ############################ 2024-03-03T23:12:36,026 # Package would be ignored # 2024-03-03T23:12:36,027 ############################ 2024-03-03T23:12:36,028 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2024-03-03T23:12:36,028 but it is absent from setuptools' `packages` configuration. 2024-03-03T23:12:36,029 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-03T23:12:36,029 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2024-03-03T23:12:36,030 to the `packages` configuration field. 2024-03-03T23:12:36,030 Alternatively, you can also rely on setuptools' discovery methods 2024-03-03T23:12:36,031 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-03T23:12:36,031 instead of `find_packages(...)`/`find:`). 2024-03-03T23:12:36,032 You can read more about "package discovery" on setuptools documentation page: 2024-03-03T23:12:36,033 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-03T23:12:36,034 If you don't want 'uncalled4.__pycache__' to be distributed and are 2024-03-03T23:12:36,034 already explicitly excluding 'uncalled4.__pycache__' via 2024-03-03T23:12:36,035 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-03T23:12:36,035 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-03T23:12:36,036 combination with a more fine grained `package-data` configuration. 2024-03-03T23:12:36,037 You can read more about "package data files" on setuptools documentation page: 2024-03-03T23:12:36,038 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-03T23:12:36,039 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-03T23:12:36,040 even if it does not contain any `.py` files. 2024-03-03T23:12:36,040 On the other hand, currently there is no concept of package data 2024-03-03T23:12:36,040 directory, all directories are treated like packages. 2024-03-03T23:12:36,041 ******************************************************************************** 2024-03-03T23:12:36,042 !! 2024-03-03T23:12:36,042 check.warn(importable) 2024-03-03T23:12:36,043 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2024-03-03T23:12:36,044 !! 2024-03-03T23:12:36,045 ******************************************************************************** 2024-03-03T23:12:36,046 ############################ 2024-03-03T23:12:36,046 # Package would be ignored # 2024-03-03T23:12:36,047 ############################ 2024-03-03T23:12:36,047 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2024-03-03T23:12:36,048 but it is absent from setuptools' `packages` configuration. 2024-03-03T23:12:36,049 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-03T23:12:36,050 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2024-03-03T23:12:36,050 to the `packages` configuration field. 2024-03-03T23:12:36,051 Alternatively, you can also rely on setuptools' discovery methods 2024-03-03T23:12:36,052 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-03T23:12:36,052 instead of `find_packages(...)`/`find:`). 2024-03-03T23:12:36,053 You can read more about "package discovery" on setuptools documentation page: 2024-03-03T23:12:36,054 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-03T23:12:36,056 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2024-03-03T23:12:36,056 already explicitly excluding 'uncalled4.io.__pycache__' via 2024-03-03T23:12:36,057 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-03T23:12:36,057 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-03T23:12:36,058 combination with a more fine grained `package-data` configuration. 2024-03-03T23:12:36,058 You can read more about "package data files" on setuptools documentation page: 2024-03-03T23:12:36,059 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-03T23:12:36,061 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-03T23:12:36,061 even if it does not contain any `.py` files. 2024-03-03T23:12:36,062 On the other hand, currently there is no concept of package data 2024-03-03T23:12:36,062 directory, all directories are treated like packages. 2024-03-03T23:12:36,062 ******************************************************************************** 2024-03-03T23:12:36,063 !! 2024-03-03T23:12:36,064 check.warn(importable) 2024-03-03T23:12:36,064 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2024-03-03T23:12:36,065 !! 2024-03-03T23:12:36,066 ******************************************************************************** 2024-03-03T23:12:36,066 ############################ 2024-03-03T23:12:36,067 # Package would be ignored # 2024-03-03T23:12:36,067 ############################ 2024-03-03T23:12:36,068 Python recognizes 'uncalled4.models' as an importable package[^1], 2024-03-03T23:12:36,068 but it is absent from setuptools' `packages` configuration. 2024-03-03T23:12:36,069 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-03T23:12:36,070 package, please make sure that 'uncalled4.models' is explicitly added 2024-03-03T23:12:36,070 to the `packages` configuration field. 2024-03-03T23:12:36,071 Alternatively, you can also rely on setuptools' discovery methods 2024-03-03T23:12:36,072 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-03T23:12:36,072 instead of `find_packages(...)`/`find:`). 2024-03-03T23:12:36,073 You can read more about "package discovery" on setuptools documentation page: 2024-03-03T23:12:36,074 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-03T23:12:36,075 If you don't want 'uncalled4.models' to be distributed and are 2024-03-03T23:12:36,076 already explicitly excluding 'uncalled4.models' via 2024-03-03T23:12:36,076 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-03T23:12:36,077 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-03T23:12:36,078 combination with a more fine grained `package-data` configuration. 2024-03-03T23:12:36,079 You can read more about "package data files" on setuptools documentation page: 2024-03-03T23:12:36,080 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-03T23:12:36,082 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-03T23:12:36,082 even if it does not contain any `.py` files. 2024-03-03T23:12:36,083 On the other hand, currently there is no concept of package data 2024-03-03T23:12:36,083 directory, all directories are treated like packages. 2024-03-03T23:12:36,084 ******************************************************************************** 2024-03-03T23:12:36,085 !! 2024-03-03T23:12:36,085 check.warn(importable) 2024-03-03T23:12:36,086 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2024-03-03T23:12:36,087 !! 2024-03-03T23:12:36,088 ******************************************************************************** 2024-03-03T23:12:36,088 ############################ 2024-03-03T23:12:36,088 # Package would be ignored # 2024-03-03T23:12:36,089 ############################ 2024-03-03T23:12:36,089 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2024-03-03T23:12:36,090 but it is absent from setuptools' `packages` configuration. 2024-03-03T23:12:36,091 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-03T23:12:36,091 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2024-03-03T23:12:36,092 to the `packages` configuration field. 2024-03-03T23:12:36,092 Alternatively, you can also rely on setuptools' discovery methods 2024-03-03T23:12:36,093 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-03T23:12:36,093 instead of `find_packages(...)`/`find:`). 2024-03-03T23:12:36,094 You can read more about "package discovery" on setuptools documentation page: 2024-03-03T23:12:36,095 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-03T23:12:36,096 If you don't want 'uncalled4.models.tombo' to be distributed and are 2024-03-03T23:12:36,096 already explicitly excluding 'uncalled4.models.tombo' via 2024-03-03T23:12:36,097 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-03T23:12:36,097 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-03T23:12:36,098 combination with a more fine grained `package-data` configuration. 2024-03-03T23:12:36,099 You can read more about "package data files" on setuptools documentation page: 2024-03-03T23:12:36,100 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-03T23:12:36,101 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-03T23:12:36,102 even if it does not contain any `.py` files. 2024-03-03T23:12:36,102 On the other hand, currently there is no concept of package data 2024-03-03T23:12:36,103 directory, all directories are treated like packages. 2024-03-03T23:12:36,103 ******************************************************************************** 2024-03-03T23:12:36,104 !! 2024-03-03T23:12:36,105 check.warn(importable) 2024-03-03T23:12:36,105 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2024-03-03T23:12:36,106 !! 2024-03-03T23:12:36,107 ******************************************************************************** 2024-03-03T23:12:36,107 ############################ 2024-03-03T23:12:36,108 # Package would be ignored # 2024-03-03T23:12:36,108 ############################ 2024-03-03T23:12:36,109 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2024-03-03T23:12:36,109 but it is absent from setuptools' `packages` configuration. 2024-03-03T23:12:36,111 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-03T23:12:36,111 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2024-03-03T23:12:36,112 to the `packages` configuration field. 2024-03-03T23:12:36,113 Alternatively, you can also rely on setuptools' discovery methods 2024-03-03T23:12:36,114 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-03T23:12:36,114 instead of `find_packages(...)`/`find:`). 2024-03-03T23:12:36,117 You can read more about "package discovery" on setuptools documentation page: 2024-03-03T23:12:36,131 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-03T23:12:36,137 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2024-03-03T23:12:36,137 already explicitly excluding 'uncalled4.stats.__pycache__' via 2024-03-03T23:12:36,138 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-03T23:12:36,138 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-03T23:12:36,139 combination with a more fine grained `package-data` configuration. 2024-03-03T23:12:36,141 You can read more about "package data files" on setuptools documentation page: 2024-03-03T23:12:36,141 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-03T23:12:36,143 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-03T23:12:36,143 even if it does not contain any `.py` files. 2024-03-03T23:12:36,144 On the other hand, currently there is no concept of package data 2024-03-03T23:12:36,144 directory, all directories are treated like packages. 2024-03-03T23:12:36,145 ******************************************************************************** 2024-03-03T23:12:36,145 !! 2024-03-03T23:12:36,146 check.warn(importable) 2024-03-03T23:12:36,146 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2024-03-03T23:12:36,147 !! 2024-03-03T23:12:36,148 ******************************************************************************** 2024-03-03T23:12:36,148 ############################ 2024-03-03T23:12:36,149 # Package would be ignored # 2024-03-03T23:12:36,149 ############################ 2024-03-03T23:12:36,150 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2024-03-03T23:12:36,151 but it is absent from setuptools' `packages` configuration. 2024-03-03T23:12:36,152 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-03T23:12:36,152 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2024-03-03T23:12:36,153 to the `packages` configuration field. 2024-03-03T23:12:36,154 Alternatively, you can also rely on setuptools' discovery methods 2024-03-03T23:12:36,154 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-03T23:12:36,155 instead of `find_packages(...)`/`find:`). 2024-03-03T23:12:36,156 You can read more about "package discovery" on setuptools documentation page: 2024-03-03T23:12:36,157 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-03T23:12:36,158 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2024-03-03T23:12:36,159 already explicitly excluding 'uncalled4.vis.__pycache__' via 2024-03-03T23:12:36,159 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-03T23:12:36,160 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-03T23:12:36,160 combination with a more fine grained `package-data` configuration. 2024-03-03T23:12:36,161 You can read more about "package data files" on setuptools documentation page: 2024-03-03T23:12:36,162 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-03T23:12:36,164 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-03T23:12:36,164 even if it does not contain any `.py` files. 2024-03-03T23:12:36,165 On the other hand, currently there is no concept of package data 2024-03-03T23:12:36,165 directory, all directories are treated like packages. 2024-03-03T23:12:36,166 ******************************************************************************** 2024-03-03T23:12:36,167 !! 2024-03-03T23:12:36,167 check.warn(importable) 2024-03-03T23:12:36,168 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2024-03-03T23:12:36,168 !! 2024-03-03T23:12:36,169 ******************************************************************************** 2024-03-03T23:12:36,170 ############################ 2024-03-03T23:12:36,170 # Package would be ignored # 2024-03-03T23:12:36,170 ############################ 2024-03-03T23:12:36,171 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2024-03-03T23:12:36,171 but it is absent from setuptools' `packages` configuration. 2024-03-03T23:12:36,172 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-03T23:12:36,172 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2024-03-03T23:12:36,173 to the `packages` configuration field. 2024-03-03T23:12:36,174 Alternatively, you can also rely on setuptools' discovery methods 2024-03-03T23:12:36,174 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-03T23:12:36,175 instead of `find_packages(...)`/`find:`). 2024-03-03T23:12:36,176 You can read more about "package discovery" on setuptools documentation page: 2024-03-03T23:12:36,177 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-03T23:12:36,178 If you don't want 'uncalled4.vis.assets' to be distributed and are 2024-03-03T23:12:36,178 already explicitly excluding 'uncalled4.vis.assets' via 2024-03-03T23:12:36,179 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-03T23:12:36,179 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-03T23:12:36,179 combination with a more fine grained `package-data` configuration. 2024-03-03T23:12:36,180 You can read more about "package data files" on setuptools documentation page: 2024-03-03T23:12:36,181 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-03T23:12:36,183 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-03T23:12:36,183 even if it does not contain any `.py` files. 2024-03-03T23:12:36,184 On the other hand, currently there is no concept of package data 2024-03-03T23:12:36,184 directory, all directories are treated like packages. 2024-03-03T23:12:36,185 ******************************************************************************** 2024-03-03T23:12:36,186 !! 2024-03-03T23:12:36,186 check.warn(importable) 2024-03-03T23:12:36,186 creating build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,187 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,188 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,188 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,188 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,189 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,189 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,190 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,191 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,191 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,192 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,192 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,193 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,193 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,193 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,194 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,194 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,195 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,195 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-03T23:12:36,196 creating build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-03T23:12:36,196 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-03T23:12:36,197 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-03T23:12:36,197 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-03T23:12:36,197 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-03T23:12:36,198 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-03T23:12:36,199 creating build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-03T23:12:36,199 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-03T23:12:36,200 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-03T23:12:36,200 creating build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,201 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,201 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,202 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,202 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,203 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,203 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,204 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,204 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,205 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,206 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,206 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,207 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,207 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,208 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-03T23:12:36,208 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,209 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,209 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,209 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,210 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,210 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,211 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,211 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,212 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,212 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,214 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,216 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,219 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,221 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,223 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,226 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-03T23:12:36,228 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-03T23:12:36,229 copying src/uncalled4/vis/assets/.browser.js.swp -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-03T23:12:36,232 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-03T23:12:36,234 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-03T23:12:36,236 creating build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,237 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,239 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,242 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,244 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,246 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,248 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,250 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,253 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,255 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,257 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-03T23:12:36,262 running build_ext 2024-03-03T23:12:36,875 building '_uncalled4' extension 2024-03-03T23:12:36,902 creating build/temp.linux-armv7l-cpython-311 2024-03-03T23:12:36,903 creating build/temp.linux-armv7l-cpython-311/src 2024-03-03T23:12:36,904 creating build/temp.linux-armv7l-cpython-311/src/cpp 2024-03-03T23:12:36,906 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/config.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/config.o -std=c++11 -O3 -g 2024-03-03T23:12:43,199 In file included from src/cpp/dtw.hpp:7, 2024-03-03T23:12:43,199 from src/cpp/config.hpp:30, 2024-03-03T23:12:43,200 from src/cpp/config.cpp:1: 2024-03-03T23:12:43,201 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:12:43,201 src/cpp/intervals.hpp:110:20: required from here 2024-03-03T23:12:43,202 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:12:43,203 192 | struct PyArray { 2024-03-03T23:12:43,203 | ^~~~~~~ 2024-03-03T23:12:43,437 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:12:43,438 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-03T23:12:43,438 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:12:43,530 In file included from src/cpp/aln.hpp:11, 2024-03-03T23:12:43,531 from src/cpp/dtw.hpp:9: 2024-03-03T23:12:43,531 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-03T23:12:43,532 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:12:43,532 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-03T23:12:43,533 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-03T23:12:43,534 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:12:43,534 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-03T23:12:43,562 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-03T23:12:43,563 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] 2024-03-03T23:12:43,564 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-03T23:12:43,564 | ~~^~~~~~~~~~ 2024-03-03T23:12:43,566 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-03T23:12:43,566 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] 2024-03-03T23:12:43,567 158 | normalize({0, events.size(), scale, shift}); 2024-03-03T23:12:43,567 | ~~~~~~~~~~~^~ 2024-03-03T23:12:43,641 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:12:43,641 src/cpp/event_detector.hpp:211:39: required from here 2024-03-03T23:12:43,642 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:12:43,642 192 | struct PyArray { 2024-03-03T23:12:43,643 | ^~~~~~~ 2024-03-03T23:12:43,767 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-03T23:12:43,767 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-03T23:12:43,768 187 | i64 ref; 2024-03-03T23:12:43,769 | ^~~ 2024-03-03T23:12:43,774 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-03T23:12:43,775 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-03T23:12:43,776 279 | int len,dist; 2024-03-03T23:12:43,776 | ^~~~ 2024-03-03T23:12:43,789 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:12:43,789 src/cpp/aln.hpp:383:23: required from here 2024-03-03T23:12:43,790 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:12:43,791 192 | struct PyArray { 2024-03-03T23:12:43,792 | ^~~~~~~ 2024-03-03T23:12:43,871 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:12:43,872 src/cpp/dtw.hpp:395:26: required from here 2024-03-03T23:12:43,873 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:13:01,298 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/dtw.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/dtw.o -std=c++11 -O3 -g 2024-03-03T23:13:07,037 In file included from src/cpp/dtw.hpp:7, 2024-03-03T23:13:07,037 from src/cpp/dtw.cpp:1: 2024-03-03T23:13:07,038 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:13:07,038 src/cpp/intervals.hpp:110:20: required from here 2024-03-03T23:13:07,039 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:13:07,040 192 | struct PyArray { 2024-03-03T23:13:07,040 | ^~~~~~~ 2024-03-03T23:13:07,274 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:13:07,275 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-03T23:13:07,276 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:13:07,367 In file included from src/cpp/aln.hpp:11, 2024-03-03T23:13:07,368 from src/cpp/dtw.hpp:9: 2024-03-03T23:13:07,368 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-03T23:13:07,369 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:13:07,369 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-03T23:13:07,370 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-03T23:13:07,370 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:13:07,371 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-03T23:13:07,399 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-03T23:13:07,400 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] 2024-03-03T23:13:07,400 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-03T23:13:07,401 | ~~^~~~~~~~~~ 2024-03-03T23:13:07,402 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-03T23:13:07,402 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] 2024-03-03T23:13:07,403 158 | normalize({0, events.size(), scale, shift}); 2024-03-03T23:13:07,404 | ~~~~~~~~~~~^~ 2024-03-03T23:13:07,477 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:13:07,478 src/cpp/event_detector.hpp:211:39: required from here 2024-03-03T23:13:07,479 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:13:07,480 192 | struct PyArray { 2024-03-03T23:13:07,480 | ^~~~~~~ 2024-03-03T23:13:07,604 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-03T23:13:07,605 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-03T23:13:07,605 187 | i64 ref; 2024-03-03T23:13:07,606 | ^~~ 2024-03-03T23:13:07,611 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-03T23:13:07,612 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-03T23:13:07,612 279 | int len,dist; 2024-03-03T23:13:07,613 | ^~~~ 2024-03-03T23:13:07,625 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:13:07,626 src/cpp/aln.hpp:383:23: required from here 2024-03-03T23:13:07,627 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:13:07,627 192 | struct PyArray { 2024-03-03T23:13:07,628 | ^~~~~~~ 2024-03-03T23:13:07,708 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:13:07,709 src/cpp/dtw.hpp:395:26: required from here 2024-03-03T23:13:07,709 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:13:07,731 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2024-03-03T23:13:07,732 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2024-03-03T23:13:07,733 21 | size_t i = 0, j = 0, b = 0; 2024-03-03T23:13:07,733 | ^ 2024-03-03T23:13:07,738 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:13:07,739 src/cpp/dtw.cpp:64:30: required from here 2024-03-03T23:13:07,740 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:13:07,740 192 | struct PyArray { 2024-03-03T23:13:07,741 | ^~~~~~~ 2024-03-03T23:13:07,748 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2024-03-03T23:13:07,749 src/cpp/dtw.cpp:98:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2024-03-03T23:13:07,749 98 | auto fill = backfill_na ? samps : Interval(); 2024-03-03T23:13:07,750 | ^~~~ 2024-03-03T23:14:07,348 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/event_detector.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/event_detector.o -std=c++11 -O3 -g 2024-03-03T23:14:13,087 In file included from src/cpp/intervals.hpp:11, 2024-03-03T23:14:13,088 from src/cpp/event_detector.hpp:13, 2024-03-03T23:14:13,089 from src/cpp/event_detector.cpp:15: 2024-03-03T23:14:13,090 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:14:13,091 src/cpp/intervals.hpp:110:20: required from here 2024-03-03T23:14:13,091 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:14:13,092 192 | struct PyArray { 2024-03-03T23:14:13,093 | ^~~~~~~ 2024-03-03T23:14:13,113 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:14:13,114 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-03T23:14:13,115 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:14:13,214 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-03T23:14:13,214 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:14:13,215 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-03T23:14:13,216 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-03T23:14:13,216 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:14:13,217 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-03T23:14:13,248 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-03T23:14:13,249 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] 2024-03-03T23:14:13,249 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-03T23:14:13,250 | ~~^~~~~~~~~~ 2024-03-03T23:14:13,251 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-03T23:14:13,252 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] 2024-03-03T23:14:13,252 158 | normalize({0, events.size(), scale, shift}); 2024-03-03T23:14:13,253 | ~~~~~~~~~~~^~ 2024-03-03T23:14:13,338 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:14:13,338 src/cpp/event_detector.hpp:211:39: required from here 2024-03-03T23:14:13,339 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:14:13,340 192 | struct PyArray { 2024-03-03T23:14:13,340 | ^~~~~~~ 2024-03-03T23:14:13,416 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:14:13,417 src/cpp/event_detector.cpp:242:30: required from here 2024-03-03T23:14:13,418 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:14:40,262 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/intervals.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/intervals.o -std=c++11 -O3 -g 2024-03-03T23:14:45,956 In file included from src/cpp/intervals.hpp:11, 2024-03-03T23:14:45,957 from src/cpp/intervals.cpp:2: 2024-03-03T23:14:45,958 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:14:45,958 src/cpp/intervals.hpp:110:20: required from here 2024-03-03T23:14:45,959 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:14:45,960 192 | struct PyArray { 2024-03-03T23:14:45,961 | ^~~~~~~ 2024-03-03T23:14:48,184 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2024-03-03T23:14:48,185 src/cpp/intervals.hpp:467:31: required from ‘static void IntervalIndex::pybind(pybind11::module_&, const std::string&) [with T = int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:14:48,186 src/cpp/intervals.cpp:7:31: required from here 2024-03-03T23:14:48,186 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] 2024-03-03T23:14:48,187 348 | while (gap >= MAX_LEN_I16) { 2024-03-03T23:14:48,188 | ~~~~^~~~~~~~~~~~~~ 2024-03-03T23:15:20,385 In file included from /usr/include/c++/12/vector:70, 2024-03-03T23:15:20,386 from src/cpp/intervals.hpp:6: 2024-03-03T23:15:20,386 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Interval&}; _Tp = Interval; _Alloc = std::allocator >]’: 2024-03-03T23:15:20,387 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-03-03T23:15:20,388 439 | vector<_Tp, _Alloc>:: 2024-03-03T23:15:20,389 | ^~~~~~~~~~~~~~~~~~~ 2024-03-03T23:15:20,482 In file included from /usr/include/c++/12/vector:64: 2024-03-03T23:15:20,483 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:20,484 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:20,484 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-03T23:15:20,485 inlined from ‘IntervalIndex IntervalIndex::mirror() const [with T = long long int]’ at src/cpp/intervals.hpp:160:23: 2024-03-03T23:15:20,485 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:20,486 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:20,486 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:20,583 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:20,583 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:20,584 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:235:23: 2024-03-03T23:15:20,585 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:20,585 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:20,586 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:20,587 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:20,587 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:20,588 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:237:27: 2024-03-03T23:15:20,589 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:20,590 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:20,590 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:20,591 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:20,591 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:20,592 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:242:19: 2024-03-03T23:15:20,592 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:20,593 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:20,594 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:20,827 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:20,827 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:20,828 inlined from ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:202:27: 2024-03-03T23:15:20,828 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:20,829 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:20,830 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:20,830 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:20,831 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:20,831 inlined from ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:212:19: 2024-03-03T23:15:20,832 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:20,832 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:20,833 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:20,938 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:20,939 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:20,939 inlined from ‘IntervalIndex IntervalIndex::intersect(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:176:31: 2024-03-03T23:15:20,940 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:20,941 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:20,941 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:34,746 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: 2024-03-03T23:15:34,775 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-03-03T23:15:34,777 439 | vector<_Tp, _Alloc>:: 2024-03-03T23:15:34,778 | ^~~~~~~~~~~~~~~~~~~ 2024-03-03T23:15:34,819 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2024-03-03T23:15:34,819 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2024-03-03T23:15:34,820 inlined from ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector, std::allocator > >; Value = std::pair]’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/stl.h:180:28: 2024-03-03T23:15:34,821 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:34,822 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-03-03T23:15:34,823 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-03T23:15:35,046 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:35,047 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:35,048 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-03T23:15:35,048 inlined from ‘void IntervalIndex::init_coords(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:134:19, 2024-03-03T23:15:35,049 inlined from ‘IntervalIndex::IntervalIndex(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:101:20, 2024-03-03T23:15:35,049 inlined from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = IntervalIndex; Args = {std::vector, std::allocator > >}; typename std::enable_if::value, int>::type = 0]’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12, 2024-03-03T23:15:35,050 inlined from ‘pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70, 2024-03-03T23:15:35,051 inlined from ‘Return pybind11::detail::argument_loader::call_impl(Func&&, pybind11::detail::index_sequence, Guard&&) && [with Return = void; Func = pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&; unsigned int ...Is = {0, 1}; Guard = pybind11::detail::void_type; Args = {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}]’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1480:37, 2024-03-03T23:15:35,052 inlined from ‘pybind11::detail::enable_if_t::value, pybind11::detail::void_type> pybind11::detail::argument_loader::call(Func&&) && [with Return = void; Guard = pybind11::detail::void_type; Func = pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&; Args = {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}]’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1454:65, 2024-03-03T23:15:35,053 inlined from ‘pybind11::cpp_function::initialize, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>, void, pybind11::detail::value_and_holder&, std::vector, std::allocator > >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor>(pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&&, void (*)(pybind11::detail::value_and_holder&, std::vector, std::allocator > >), const pybind11::name&, const pybind11::is_method&, const pybind11::sibling&, const pybind11::detail::is_new_style_constructor&)::’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:250:78, 2024-03-03T23:15:35,053 inlined from ‘static pybind11::handle pybind11::cpp_function::initialize, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>, void, pybind11::detail::value_and_holder&, std::vector, std::allocator > >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor>(pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&&, void (*)(pybind11::detail::value_and_holder&, std::vector, std::allocator > >), const pybind11::name&, const pybind11::is_method&, const pybind11::sibling&, const pybind11::detail::is_new_style_constructor&)::::_FUN(pybind11::detail::function_call&)’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:224:21: 2024-03-03T23:15:35,054 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:35,055 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:35,055 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:35,056 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-03T23:15:35,057 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-03T23:15:35,057 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-03T23:15:35,058 inlined from ‘void IntervalIndex::init_coords(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:134:19, 2024-03-03T23:15:35,058 inlined from ‘IntervalIndex::IntervalIndex(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:101:20, 2024-03-03T23:15:35,059 inlined from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = IntervalIndex; Args = {std::vector, std::allocator > >}; typename std::enable_if::value, int>::type = 0]’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12, 2024-03-03T23:15:35,059 inlined from ‘pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70, 2024-03-03T23:15:35,060 inlined from ‘Return pybind11::detail::argument_loader::call_impl(Func&&, pybind11::detail::index_sequence, Guard&&) && [with Return = void; Func = pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&; unsigned int ...Is = {0, 1}; Guard = pybind11::detail::void_type; Args = {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}]’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1480:37, 2024-03-03T23:15:35,061 inlined from ‘pybind11::detail::enable_if_t::value, pybind11::detail::void_type> pybind11::detail::argument_loader::call(Func&&) && [with Return = void; Guard = pybind11::detail::void_type; Func = pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&; Args = {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}]’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1454:65, 2024-03-03T23:15:35,062 inlined from ‘pybind11::cpp_function::initialize, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>, void, pybind11::detail::value_and_holder&, std::vector, std::allocator > >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor>(pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&&, void (*)(pybind11::detail::value_and_holder&, std::vector, std::allocator > >), const pybind11::name&, const pybind11::is_method&, const pybind11::sibling&, const pybind11::detail::is_new_style_constructor&)::’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:254:75, 2024-03-03T23:15:35,063 inlined from ‘static pybind11::handle pybind11::cpp_function::initialize, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>, void, pybind11::detail::value_and_holder&, std::vector, std::allocator > >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor>(pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&&, void (*)(pybind11::detail::value_and_holder&, std::vector, std::allocator > >), const pybind11::name&, const pybind11::is_method&, const pybind11::sibling&, const pybind11::detail::is_new_style_constructor&)::::_FUN(pybind11::detail::function_call&)’ at /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:224:21: 2024-03-03T23:15:35,063 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-03T23:15:35,064 1287 | _M_realloc_insert(end(), __x); 2024-03-03T23:15:35,065 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-03T23:15:45,800 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/normalizer.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/normalizer.o -std=c++11 -O3 -g 2024-03-03T23:15:58,680 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/pore_model.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/pore_model.o -std=c++11 -O3 -g 2024-03-03T23:16:04,388 In file included from src/cpp/pore_model.hpp:36, 2024-03-03T23:16:04,388 from src/cpp/pore_model.cpp:1: 2024-03-03T23:16:04,389 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:04,389 src/cpp/intervals.hpp:110:20: required from here 2024-03-03T23:16:04,390 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:04,391 192 | struct PyArray { 2024-03-03T23:16:04,391 | ^~~~~~~ 2024-03-03T23:16:40,306 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/pybinder.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/pybinder.o -std=c++11 -O3 -g 2024-03-03T23:16:46,086 In file included from src/cpp/read_buffer.hpp:30, 2024-03-03T23:16:46,087 from src/cpp/pybinder.cpp:5: 2024-03-03T23:16:46,088 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:46,089 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-03T23:16:46,089 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:46,090 192 | struct PyArray { 2024-03-03T23:16:46,091 | ^~~~~~~ 2024-03-03T23:16:46,122 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:46,123 src/cpp/intervals.hpp:110:20: required from here 2024-03-03T23:16:46,124 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:46,225 In file included from src/cpp/signal_processor.hpp:7, 2024-03-03T23:16:46,225 from src/cpp/pybinder.cpp:6: 2024-03-03T23:16:46,226 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-03T23:16:46,226 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:16:46,227 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-03T23:16:46,228 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-03T23:16:46,228 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:16:46,229 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-03T23:16:46,278 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-03T23:16:46,278 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] 2024-03-03T23:16:46,279 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-03T23:16:46,279 | ~~^~~~~~~~~~ 2024-03-03T23:16:46,281 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-03T23:16:46,281 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] 2024-03-03T23:16:46,282 158 | normalize({0, events.size(), scale, shift}); 2024-03-03T23:16:46,282 | ~~~~~~~~~~~^~ 2024-03-03T23:16:46,356 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:46,357 src/cpp/event_detector.hpp:211:39: required from here 2024-03-03T23:16:46,357 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:46,358 192 | struct PyArray { 2024-03-03T23:16:46,359 | ^~~~~~~ 2024-03-03T23:16:46,664 In file included from src/cpp/dtw.hpp:9, 2024-03-03T23:16:46,665 from src/cpp/pybinder.cpp:8: 2024-03-03T23:16:46,666 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-03T23:16:46,666 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-03T23:16:46,667 187 | i64 ref; 2024-03-03T23:16:46,667 | ^~~ 2024-03-03T23:16:46,670 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-03T23:16:46,671 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-03T23:16:46,672 279 | int len,dist; 2024-03-03T23:16:46,672 | ^~~~ 2024-03-03T23:16:46,683 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:46,684 src/cpp/aln.hpp:383:23: required from here 2024-03-03T23:16:46,684 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:46,685 192 | struct PyArray { 2024-03-03T23:16:46,686 | ^~~~~~~ 2024-03-03T23:16:46,764 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:46,764 src/cpp/dtw.hpp:395:26: required from here 2024-03-03T23:16:46,765 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:46,808 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:46,809 src/cpp/eventalign.hpp:110:31: required from here 2024-03-03T23:16:46,809 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:50,551 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:50,551 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const std::string&, pybind11::array_t, bool, pybind11::array_t, pybind11::array_t, pybind11::array_t, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string; typename ModelType::kmer_t = short unsigned int]’ 2024-03-03T23:16:50,552 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]’ 2024-03-03T23:16:50,553 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:16:50,553 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:50,582 In file included from src/cpp/pybinder.cpp:10: 2024-03-03T23:16:50,583 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]’: 2024-03-03T23:16:50,583 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]’ 2024-03-03T23:16:50,584 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:16:50,584 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:16:50,585 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-03T23:16:50,585 | ~~^~~~~~~~~~~ 2024-03-03T23:16:50,757 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-03T23:16:50,758 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const std::string&, pybind11::array_t, bool, pybind11::array_t, pybind11::array_t, pybind11::array_t, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string; typename ModelType::kmer_t = unsigned int]’ 2024-03-03T23:16:50,759 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]’ 2024-03-03T23:16:50,759 src/cpp/pybinder.cpp:67:22: required from here 2024-03-03T23:16:50,760 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-03T23:16:50,761 192 | struct PyArray { 2024-03-03T23:16:50,762 | ^~~~~~~ 2024-03-03T23:16:50,787 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]’: 2024-03-03T23:16:50,787 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]’ 2024-03-03T23:16:50,788 src/cpp/pybinder.cpp:67:22: required from here 2024-03-03T23:16:50,789 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-03T23:16:50,789 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-03T23:16:50,790 | ~~^~~~~~~~~~~ 2024-03-03T23:16:57,570 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-03T23:16:57,571 src/cpp/dtw.hpp:734:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:16:57,571 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]’ 2024-03-03T23:16:57,572 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:16:57,573 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-03T23:16:57,573 644 | if (q0 >= qry_size()) { 2024-03-03T23:16:57,574 | ~~~^~~~~~~~~~~~~ 2024-03-03T23:16:57,575 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-03T23:16:57,575 651 | if (r1 > ref_size()) { 2024-03-03T23:16:57,576 | ~~~^~~~~~~~~~~~ 2024-03-03T23:16:58,079 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-03T23:16:58,080 src/cpp/dtw.hpp:734:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:16:58,081 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]’ 2024-03-03T23:16:58,081 src/cpp/pybinder.cpp:67:22: required from here 2024-03-03T23:16:58,082 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-03T23:16:58,083 644 | if (q0 >= qry_size()) { 2024-03-03T23:16:58,083 | ~~~^~~~~~~~~~~~~ 2024-03-03T23:16:58,084 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-03T23:16:58,085 651 | if (r1 > ref_size()) { 2024-03-03T23:16:58,085 | ~~~^~~~~~~~~~~~ 2024-03-03T23:17:08,940 In file included from src/cpp/seq.hpp:32, 2024-03-03T23:17:08,941 from src/cpp/pybinder.cpp:7: 2024-03-03T23:17:08,941 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]’: 2024-03-03T23:17:08,942 src/cpp/pore_model.hpp:496:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:08,943 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:08,943 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:08,944 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]’ 2024-03-03T23:17:08,945 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:17:08,946 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-03T23:17:08,947 507 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2024-03-03T23:17:08,947 | ~~~~~~~~~~^ 2024-03-03T23:17:08,948 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]’: 2024-03-03T23:17:08,948 src/cpp/pore_model.hpp:498:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:08,949 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:08,949 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:08,950 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]’ 2024-03-03T23:17:08,950 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:17:08,951 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-03T23:17:11,590 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]’: 2024-03-03T23:17:11,591 src/cpp/pore_model.hpp:496:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:11,591 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:11,592 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:11,593 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]’ 2024-03-03T23:17:11,594 src/cpp/pybinder.cpp:67:22: required from here 2024-03-03T23:17:11,594 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-03T23:17:11,595 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]’: 2024-03-03T23:17:11,595 src/cpp/pore_model.hpp:498:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:11,596 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:11,597 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:11,598 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]’ 2024-03-03T23:17:11,598 src/cpp/pybinder.cpp:67:22: required from here 2024-03-03T23:17:11,599 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-03T23:17:18,791 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]’: 2024-03-03T23:17:18,791 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-03T23:17:18,792 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-03T23:17:18,793 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-03T23:17:18,793 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.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 = {}]’ 2024-03-03T23:17:18,794 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:18,795 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]’ 2024-03-03T23:17:18,796 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:17:18,797 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-03T23:17:18,797 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-03T23:17:18,798 | ^~~~~~~~ 2024-03-03T23:17:19,489 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-03T23:17:19,490 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]’ 2024-03-03T23:17:19,490 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-03T23:17:19,491 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-03T23:17:19,492 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.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 = {}]’ 2024-03-03T23:17:19,492 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:19,493 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]’ 2024-03-03T23:17:19,494 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:17:19,495 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] 2024-03-03T23:17:19,495 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-03T23:17:19,496 | ~~^~~~~~~~~~~~ 2024-03-03T23:17:19,497 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-03T23:17:19,498 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]’ 2024-03-03T23:17:19,499 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-03T23:17:19,499 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-03T23:17:19,500 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.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 = {}]’ 2024-03-03T23:17:19,501 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:19,501 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]’ 2024-03-03T23:17:19,502 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:17:19,503 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] 2024-03-03T23:17:19,503 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-03T23:17:19,504 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-03T23:17:20,293 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]’: 2024-03-03T23:17:20,294 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2024-03-03T23:17:20,294 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-03T23:17:20,295 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-03T23:17:20,296 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.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 = {}]’ 2024-03-03T23:17:20,296 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:20,297 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]’ 2024-03-03T23:17:20,298 src/cpp/pybinder.cpp:67:22: required from here 2024-03-03T23:17:20,298 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-03T23:17:20,299 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-03T23:17:20,300 | ^~~~~~~~ 2024-03-03T23:17:20,487 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-03T23:17:20,488 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]’ 2024-03-03T23:17:20,488 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-03T23:17:20,489 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-03T23:17:20,489 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.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 = {}]’ 2024-03-03T23:17:20,490 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:20,491 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]’ 2024-03-03T23:17:20,492 src/cpp/pybinder.cpp:67:22: required from here 2024-03-03T23:17:20,493 src/cpp/dtw.hpp:443:33: warning: comparison of integer expressions of different signedness: ‘i32’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-03T23:17:20,493 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-03T23:17:20,494 | ~~^~~~~~~~~~~~ 2024-03-03T23:17:20,494 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-03T23:17:20,495 src/cpp/dtw.hpp:357:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = unsigned int]’ 2024-03-03T23:17:20,495 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-03T23:17:20,496 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-03T23:17:20,496 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.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 = {}]’ 2024-03-03T23:17:20,497 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:20,498 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]’ 2024-03-03T23:17:20,499 src/cpp/pybinder.cpp:67:22: required from here 2024-03-03T23:17:20,499 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] 2024-03-03T23:17:20,500 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-03T23:17:20,500 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-03T23:17:21,612 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2024-03-03T23:17:21,613 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]’ 2024-03-03T23:17:21,614 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-03T23:17:21,615 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-03T23:17:21,616 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-03T23:17:21,616 /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/.eggs/pybind11-2.11.1-py3.11.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 = {}]’ 2024-03-03T23:17:21,617 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-03T23:17:21,618 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]’ 2024-03-03T23:17:21,618 src/cpp/pybinder.cpp:66:22: required from here 2024-03-03T23:17:21,619 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2024-03-03T23:17:21,620 144 | auto sum = super::sum(); 2024-03-03T23:17:21,620 | ^~~ 2024-03-03T23:17:21,621 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2024-03-03T23:17:21,622 145 | auto len = super::size(); 2024-03-03T23:17:21,623 | ^~~ 2024-03-03T23:18:08,821 virtual memory exhausted: Cannot allocate memory 2024-03-03T23:18:08,949 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-03-03T23:18:09,104 ERROR: python setup.py bdist_wheel exited with 1 2024-03-03T23:18:09,118 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2024-03-03T23:18:09,118 exec(compile('"'"''"'"''"'"' 2024-03-03T23:18:09,118 # This is -- a caller that pip uses to run setup.py 2024-03-03T23:18:09,118 # 2024-03-03T23:18:09,118 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-03-03T23:18:09,118 # import from `distutils.core` to work with newer packaging standards. 2024-03-03T23:18:09,118 # - It provides a clear error message when setuptools is not installed. 2024-03-03T23:18:09,118 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-03-03T23:18:09,118 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-03-03T23:18:09,118 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-03-03T23:18:09,118 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-03-03T23:18:09,118 import os, sys, tokenize 2024-03-03T23:18:09,118 2024-03-03T23:18:09,118 try: 2024-03-03T23:18:09,118 import setuptools 2024-03-03T23:18:09,118 except ImportError as error: 2024-03-03T23:18:09,118 print( 2024-03-03T23:18:09,118 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-03-03T23:18:09,118 "the build environment.", 2024-03-03T23:18:09,118 file=sys.stderr, 2024-03-03T23:18:09,118 ) 2024-03-03T23:18:09,118 sys.exit(1) 2024-03-03T23:18:09,118 2024-03-03T23:18:09,118 __file__ = %r 2024-03-03T23:18:09,118 sys.argv[0] = __file__ 2024-03-03T23:18:09,118 2024-03-03T23:18:09,118 if os.path.exists(__file__): 2024-03-03T23:18:09,118 filename = __file__ 2024-03-03T23:18:09,118 with tokenize.open(__file__) as f: 2024-03-03T23:18:09,118 setup_py_code = f.read() 2024-03-03T23:18:09,118 else: 2024-03-03T23:18:09,118 filename = "" 2024-03-03T23:18:09,118 setup_py_code = "from setuptools import setup; setup()" 2024-03-03T23:18:09,118 2024-03-03T23:18:09,118 exec(compile(setup_py_code, filename, "exec")) 2024-03-03T23:18:09,118 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-wg7ivqnv[/] 2024-03-03T23:18:09,118 [bold magenta]cwd[/]: /tmp/pip-wheel-gnyb8mtt/uncalled4_ddb89b7fa5f0421db7ebda411fd7f3b0/ 2024-03-03T23:18:09,119 Building wheel for uncalled4 (setup.py): finished with status 'error' 2024-03-03T23:18:09,120 ERROR: Failed building wheel for uncalled4 2024-03-03T23:18:09,121 Running setup.py clean for uncalled4 2024-03-03T23:18:09,123 Running command python setup.py clean 2024-03-03T23:18:10,053 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-03T23:18:10,053 !! 2024-03-03T23:18:10,055 ******************************************************************************** 2024-03-03T23:18:10,055 Requirements should be satisfied by a PEP 517 installer. 2024-03-03T23:18:10,056 If you are using pip, you can try `pip install --use-pep517`. 2024-03-03T23:18:10,057 ******************************************************************************** 2024-03-03T23:18:10,058 !! 2024-03-03T23:18:10,058 dist.fetch_build_eggs(dist.setup_requires) 2024-03-03T23:18:10,279 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-03T23:18:10,280 warnings.warn(msg) 2024-03-03T23:18:10,472 running clean 2024-03-03T23:18:10,525 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2024-03-03T23:18:10,537 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2024-03-03T23:18:10,566 'build/bdist.linux-armv7l' does not exist -- can't clean it 2024-03-03T23:18:10,566 'build/scripts-3.11' does not exist -- can't clean it 2024-03-03T23:18:10,567 removing 'build' 2024-03-03T23:18:10,683 Failed to build uncalled4 2024-03-03T23:18:10,685 ERROR: Failed to build one or more wheels 2024-03-03T23:18:10,686 Exception information: 2024-03-03T23:18:10,686 Traceback (most recent call last): 2024-03-03T23:18:10,686 File "/home/piwheels/.local/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2024-03-03T23:18:10,686 status = run_func(*args) 2024-03-03T23:18:10,686 ^^^^^^^^^^^^^^^ 2024-03-03T23:18:10,686 File "/home/piwheels/.local/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2024-03-03T23:18:10,686 return func(self, options, args) 2024-03-03T23:18:10,686 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-03T23:18:10,686 File "/home/piwheels/.local/lib/python3.11/site-packages/pip/_internal/commands/wheel.py", line 181, in run 2024-03-03T23:18:10,686 raise CommandError("Failed to build one or more wheels") 2024-03-03T23:18:10,686 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-03-03T23:18:10,690 Removed build tracker: '/tmp/pip-build-tracker-l5oju6vo'