2022-12-01T12:46:26,925 Created temporary directory: /tmp/pip-ephem-wheel-cache-j7msigjj 2022-12-01T12:46:26,928 Created temporary directory: /tmp/pip-build-tracker-4bddtjsy 2022-12-01T12:46:26,928 Initialized build tracking at /tmp/pip-build-tracker-4bddtjsy 2022-12-01T12:46:26,928 Created build tracker: /tmp/pip-build-tracker-4bddtjsy 2022-12-01T12:46:26,928 Entered build tracker: /tmp/pip-build-tracker-4bddtjsy 2022-12-01T12:46:26,929 Created temporary directory: /tmp/pip-wheel-0uwx8eh3 2022-12-01T12:46:26,932 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2022-12-01T12:46:26,935 Created temporary directory: /tmp/pip-ephem-wheel-cache-83z9n2kl 2022-12-01T12:46:26,961 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-12-01T12:46:26,965 2 location(s) to search for versions of whatshap: 2022-12-01T12:46:26,965 * https://pypi.org/simple/whatshap/ 2022-12-01T12:46:26,965 * https://www.piwheels.org/simple/whatshap/ 2022-12-01T12:46:26,965 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2022-12-01T12:46:26,966 Getting page https://pypi.org/simple/whatshap/ 2022-12-01T12:46:26,967 Found index url https://pypi.org/simple 2022-12-01T12:46:27,023 Fetched page https://pypi.org/simple/whatshap/ as application/vnd.pypi.simple.v1+json 2022-12-01T12:46:27,034 Found link https://files.pythonhosted.org/packages/35/95/43ff2304cd59ade39e64aadaeaec48e8c12bbe6262bcbbbd7b7d89487757/whatshap-0.9.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.9 2022-12-01T12:46:27,035 Found link https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.10 2022-12-01T12:46:27,035 Found link https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.11 2022-12-01T12:46:27,035 Found link https://files.pythonhosted.org/packages/01/84/31a5ea338647d0256a4a5c57e98d7a563f387e6a47f1e26299b89e3f2da1/whatshap-0.12.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.12 2022-12-01T12:46:27,035 Found link https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz (from https://pypi.org/simple/whatshap/), version: 0.13 2022-12-01T12:46:27,036 Found link 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https://files.pythonhosted.org/packages/19/36/1423d4adb6f4d7e58f5fdf8c59aaa8b5cec9d73bb5b2450f17f4089e8438/whatshap-1.2.1-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-12-01T12:46:27,043 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/3f/9c/52ce1b726a9b98f628c468b30877edc720c6c8022ae0d13fee6088f894b6/whatshap-1.2.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-12-01T12:46:27,043 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/22/c1/d7295d4b3732dc286990b85348401b3bf932bdcb196162f14100472683f3/whatshap-1.2.1-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6) 2022-12-01T12:46:27,043 Skipping link: No binaries permitted for whatshap: 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https://files.pythonhosted.org/packages/3f/86/778bbef5c06bdf48c738fdcd64c0a947398d78a168d1dfc949fc7665afa2/whatshap-1.6-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2022-12-01T12:46:27,049 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/9d/60/749fe7dcbb28f21abc3190a171443c8f78d7a20a1a1dfac592966fb55dc4/whatshap-1.6-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2022-12-01T12:46:27,049 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/cd/76/28f1ce30b1cf0a26eae2a508d057b78425595104780955b36e938ac7fcbe/whatshap-1.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2022-12-01T12:46:27,050 Found link 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https://files.pythonhosted.org/packages/c1/34/785976fd423c187d90e2be419af906a366c038a57503e2e4fb6599aca868/whatshap-1.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2022-12-01T12:46:27,051 Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/e1/81/8eaf7be1255b732643ce82307a72b015230b14842a15fc83b17bd264282d/whatshap-1.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7) 2022-12-01T12:46:27,051 Found link https://files.pythonhosted.org/packages/1f/44/d11315edea202d6399af062186a30ba12a17c489115f56ed417e25921453/whatshap-1.7.tar.gz (from https://pypi.org/simple/whatshap/) (requires-python:>=3.7), version: 1.7 2022-12-01T12:46:27,051 Fetching project page and analyzing links: https://www.piwheels.org/simple/whatshap/ 2022-12-01T12:46:27,052 Getting page https://www.piwheels.org/simple/whatshap/ 2022-12-01T12:46:27,053 Found index url https://www.piwheels.org/simple 2022-12-01T12:46:27,288 Fetched page https://www.piwheels.org/simple/whatshap/ as text/html 2022-12-01T12:46:27,302 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp37-cp37m-linux_armv7l.whl#sha256=b81040280694883d7079a4b3e449bba14fc4d30f293e9a1d76a1e0578ac01cba (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-12-01T12:46:27,302 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp37-cp37m-linux_armv6l.whl#sha256=b81040280694883d7079a4b3e449bba14fc4d30f293e9a1d76a1e0578ac01cba (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-12-01T12:46:27,302 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp34-cp34m-linux_armv6l.whl#sha256=226c2159db0239fcad3b0d9731ae11ad7f161e18a0f51b5d76fbb7aa02bc5b12 (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-12-01T12:46:27,302 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp34-cp34m-linux_armv7l.whl#sha256=226c2159db0239fcad3b0d9731ae11ad7f161e18a0f51b5d76fbb7aa02bc5b12 (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-12-01T12:46:27,303 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp35-cp35m-linux_armv6l.whl#sha256=a01e2ba831e1062cac18678005ed864422821a147a90381d1d561db6daaa240b (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-12-01T12:46:27,303 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.18-cp35-cp35m-linux_armv7l.whl#sha256=a01e2ba831e1062cac18678005ed864422821a147a90381d1d561db6daaa240b (from https://www.piwheels.org/simple/whatshap/) (requires-python:>=3.4) 2022-12-01T12:46:27,303 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp37-cp37m-linux_armv6l.whl#sha256=a52131a2cecf121ac6b1d8a2f3d6b6f81722f159121dddb88c43589f05db1c48 (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,303 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp37-cp37m-linux_armv7l.whl#sha256=a52131a2cecf121ac6b1d8a2f3d6b6f81722f159121dddb88c43589f05db1c48 (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,303 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.17-cp35-cp35m-linux_armv6l.whl#sha256=bcc411757fef61409f32f77b8b87266850cb245c80f7e55030a701e7e8f9aaf2 (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,304 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,305 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.16-cp34-cp34m-linux_armv6l.whl#sha256=f220db8040faaacd90867ade6d504314e1412588bf15490cd43486b80012a5cb (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,305 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.16-cp35-cp35m-linux_armv6l.whl#sha256=e89c850742d969409e79942e188b0ccef03000e5991929a628b61e75ccf48baa (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,305 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.16-cp35-cp35m-linux_armv7l.whl#sha256=e89c850742d969409e79942e188b0ccef03000e5991929a628b61e75ccf48baa (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,305 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,306 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.15-cp34-cp34m-linux_armv7l.whl#sha256=8a603d7a9a636e78f0f8297e9ad41b9b829dc8bb2bed01428406d595852b7bb8 (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,306 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.15-cp34-cp34m-linux_armv6l.whl#sha256=8a603d7a9a636e78f0f8297e9ad41b9b829dc8bb2bed01428406d595852b7bb8 (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,306 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14.1-cp34-cp34m-linux_armv6l.whl#sha256=22ddc6e868a47bcdfd91808303be8ad0d952e65ae74767ea3d49bdd16cdfb4f2 (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,307 Skipping link: No binaries permitted for whatshap: 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(from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,307 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14-cp35-cp35m-linux_armv7l.whl#sha256=e0ac1dca2abae0b88b1fa764b4d4ca853bb6bc4b02de20b09e8d51448b20aafc (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,308 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14-cp34-cp34m-linux_armv6l.whl#sha256=3ddde88fb4fed1664ec3d46039aca72142fa5dcde177a40f49c2cec09b407f9f (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,308 Skipping link: No binaries permitted for whatshap: https://www.piwheels.org/simple/whatshap/whatshap-0.14-cp34-cp34m-linux_armv7l.whl#sha256=3ddde88fb4fed1664ec3d46039aca72142fa5dcde177a40f49c2cec09b407f9f (from https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,308 Skipping link: No binaries permitted for whatshap: 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https://www.piwheels.org/simple/whatshap/) 2022-12-01T12:46:27,312 Skipping link: not a file: https://www.piwheels.org/simple/whatshap/ 2022-12-01T12:46:27,312 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2022-12-01T12:46:27,332 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2022-12-01T12:46:27,349 Collecting whatshap==1.7 2022-12-01T12:46:27,351 Created temporary directory: /tmp/pip-unpack-xxm54c6y 2022-12-01T12:46:27,397 Downloading whatshap-1.7.tar.gz (5.4 MB) 2022-12-01T12:46:28,940 Added whatshap==1.7 from https://files.pythonhosted.org/packages/1f/44/d11315edea202d6399af062186a30ba12a17c489115f56ed417e25921453/whatshap-1.7.tar.gz to build tracker '/tmp/pip-build-tracker-4bddtjsy' 2022-12-01T12:46:28,946 Created temporary directory: /tmp/pip-build-env-3vr4bnzj 2022-12-01T12:46:28,953 Installing build dependencies: started 2022-12-01T12:46:28,954 Running command pip subprocess to install build dependencies 2022-12-01T12:46:30,144 Using pip 22.3 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2022-12-01T12:46:30,540 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2022-12-01T12:46:30,564 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-12-01T12:46:32,186 Collecting setuptools>=60 2022-12-01T12:46:32,300 Using cached https://www.piwheels.org/simple/setuptools/setuptools-65.6.3-py3-none-any.whl (1.2 MB) 2022-12-01T12:46:32,709 Collecting setuptools_scm 2022-12-01T12:46:32,765 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-7.0.5-py3-none-any.whl (42 kB) 2022-12-01T12:46:34,096 Collecting cython~=0.29.20 2022-12-01T12:46:34,576 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.32-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-12-01T12:46:34,869 Collecting tomli>=1.0.0 2022-12-01T12:46:34,887 Using cached https://www.piwheels.org/simple/tomli/tomli-2.0.1-py3-none-any.whl (12 kB) 2022-12-01T12:46:35,053 Collecting packaging>=20.0 2022-12-01T12:46:35,071 Using cached https://www.piwheels.org/simple/packaging/packaging-21.3-py3-none-any.whl (40 kB) 2022-12-01T12:46:35,172 Collecting typing-extensions 2022-12-01T12:46:35,189 Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.4.0-py3-none-any.whl (26 kB) 2022-12-01T12:46:35,448 Collecting pyparsing!=3.0.5,>=2.0.2 2022-12-01T12:46:35,467 Using cached https://www.piwheels.org/simple/pyparsing/pyparsing-3.0.9-py3-none-any.whl (98 kB) 2022-12-01T12:46:37,501 Installing collected packages: typing-extensions, tomli, setuptools, pyparsing, cython, packaging, setuptools_scm 2022-12-01T12:46:43,326 Creating /tmp/pip-build-env-3vr4bnzj/overlay/bin 2022-12-01T12:46:43,328 changing mode of /tmp/pip-build-env-3vr4bnzj/overlay/bin/cygdb to 755 2022-12-01T12:46:43,330 changing mode of /tmp/pip-build-env-3vr4bnzj/overlay/bin/cython to 755 2022-12-01T12:46:43,333 changing mode of /tmp/pip-build-env-3vr4bnzj/overlay/bin/cythonize to 755 2022-12-01T12:46:43,674 Successfully installed cython-0.29.32 packaging-21.3 pyparsing-3.0.9 setuptools-65.6.3 setuptools_scm-7.0.5 tomli-2.0.1 typing-extensions-4.4.0 2022-12-01T12:46:43,690 [notice] A new release of pip available: 22.3 -> 22.3.1 2022-12-01T12:46:43,690 [notice] To update, run: python3 -m pip install --upgrade pip 2022-12-01T12:46:44,032 Installing build dependencies: finished with status 'done' 2022-12-01T12:46:44,038 Getting requirements to build wheel: started 2022-12-01T12:46:44,039 Running command Getting requirements to build wheel 2022-12-01T12:46:52,496 warning: whatshap/priorityqueue.pyx:201:7: Unreachable code 2022-12-01T12:46:53,974 Compiling whatshap/core.pyx because it depends on /tmp/pip-build-env-3vr4bnzj/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-12-01T12:46:53,974 Compiling whatshap/polyphase/solver.pyx because it depends on /tmp/pip-build-env-3vr4bnzj/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-12-01T12:46:53,974 Compiling whatshap/readselect.pyx because it depends on /tmp/pip-build-env-3vr4bnzj/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-12-01T12:46:53,974 Compiling whatshap/priorityqueue.pyx because it depends on /tmp/pip-build-env-3vr4bnzj/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-12-01T12:46:53,975 Compiling whatshap/align.pyx because it depends on /tmp/pip-build-env-3vr4bnzj/overlay/lib/python3.9/site-packages/Cython/Includes/libc/__init__.pxd. 2022-12-01T12:46:53,975 [1/5] Cythonizing whatshap/align.pyx 2022-12-01T12:46:53,975 [2/5] Cythonizing whatshap/core.pyx 2022-12-01T12:46:53,975 [3/5] Cythonizing whatshap/polyphase/solver.pyx 2022-12-01T12:46:53,975 [4/5] Cythonizing whatshap/priorityqueue.pyx 2022-12-01T12:46:53,975 [5/5] Cythonizing whatshap/readselect.pyx 2022-12-01T12:46:54,216 running egg_info 2022-12-01T12:46:54,226 writing whatshap.egg-info/PKG-INFO 2022-12-01T12:46:54,228 writing dependency_links to whatshap.egg-info/dependency_links.txt 2022-12-01T12:46:54,231 writing entry points to whatshap.egg-info/entry_points.txt 2022-12-01T12:46:54,232 writing requirements to whatshap.egg-info/requires.txt 2022-12-01T12:46:54,234 writing top-level names to whatshap.egg-info/top_level.txt 2022-12-01T12:46:54,294 listing git files failed - pretending there aren't any 2022-12-01T12:46:54,308 reading manifest file 'whatshap.egg-info/SOURCES.txt' 2022-12-01T12:46:54,364 reading manifest template 'MANIFEST.in' 2022-12-01T12:46:54,378 adding license file 'LICENSE' 2022-12-01T12:46:54,396 writing manifest file 'whatshap.egg-info/SOURCES.txt' 2022-12-01T12:46:55,342 Getting requirements to build wheel: finished with status 'done' 2022-12-01T12:46:55,362 Installing backend dependencies: started 2022-12-01T12:46:55,363 Running command pip subprocess to install backend dependencies 2022-12-01T12:46:56,560 Using pip 22.3 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2022-12-01T12:46:56,960 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2022-12-01T12:46:56,986 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-12-01T12:46:57,423 Collecting wheel 2022-12-01T12:46:57,460 Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB) 2022-12-01T12:46:59,095 Installing collected packages: wheel 2022-12-01T12:46:59,237 Creating /tmp/pip-build-env-3vr4bnzj/normal/bin 2022-12-01T12:46:59,240 changing mode of /tmp/pip-build-env-3vr4bnzj/normal/bin/wheel to 755 2022-12-01T12:46:59,253 Successfully installed wheel-0.38.4 2022-12-01T12:46:59,268 [notice] A new release of pip available: 22.3 -> 22.3.1 2022-12-01T12:46:59,268 [notice] To update, run: python3 -m pip install --upgrade pip 2022-12-01T12:46:59,480 Installing backend dependencies: finished with status 'done' 2022-12-01T12:46:59,483 Created temporary directory: /tmp/pip-modern-metadata-byahi94d 2022-12-01T12:46:59,486 Preparing metadata (pyproject.toml): started 2022-12-01T12:46:59,487 Running command Preparing metadata (pyproject.toml) 2022-12-01T12:47:01,238 running dist_info 2022-12-01T12:47:01,260 creating /tmp/pip-modern-metadata-byahi94d/whatshap.egg-info 2022-12-01T12:47:01,267 writing /tmp/pip-modern-metadata-byahi94d/whatshap.egg-info/PKG-INFO 2022-12-01T12:47:01,269 writing dependency_links to /tmp/pip-modern-metadata-byahi94d/whatshap.egg-info/dependency_links.txt 2022-12-01T12:47:01,272 writing entry points to /tmp/pip-modern-metadata-byahi94d/whatshap.egg-info/entry_points.txt 2022-12-01T12:47:01,273 writing requirements to /tmp/pip-modern-metadata-byahi94d/whatshap.egg-info/requires.txt 2022-12-01T12:47:01,274 writing top-level names to /tmp/pip-modern-metadata-byahi94d/whatshap.egg-info/top_level.txt 2022-12-01T12:47:01,276 writing manifest file '/tmp/pip-modern-metadata-byahi94d/whatshap.egg-info/SOURCES.txt' 2022-12-01T12:47:01,336 listing git files failed - pretending there aren't any 2022-12-01T12:47:01,347 reading manifest file '/tmp/pip-modern-metadata-byahi94d/whatshap.egg-info/SOURCES.txt' 2022-12-01T12:47:01,351 reading manifest template 'MANIFEST.in' 2022-12-01T12:47:01,374 adding license file 'LICENSE' 2022-12-01T12:47:01,382 writing manifest file '/tmp/pip-modern-metadata-byahi94d/whatshap.egg-info/SOURCES.txt' 2022-12-01T12:47:01,383 creating '/tmp/pip-modern-metadata-byahi94d/whatshap-1.7.dist-info' 2022-12-01T12:47:01,665 Preparing metadata (pyproject.toml): finished with status 'done' 2022-12-01T12:47:01,672 Source in /tmp/pip-wheel-0uwx8eh3/whatshap_ad7b9343fa64467b840037bc2353ff2f has version 1.7, which satisfies requirement whatshap==1.7 from https://files.pythonhosted.org/packages/1f/44/d11315edea202d6399af062186a30ba12a17c489115f56ed417e25921453/whatshap-1.7.tar.gz 2022-12-01T12:47:01,673 Removed whatshap==1.7 from https://files.pythonhosted.org/packages/1f/44/d11315edea202d6399af062186a30ba12a17c489115f56ed417e25921453/whatshap-1.7.tar.gz from build tracker '/tmp/pip-build-tracker-4bddtjsy' 2022-12-01T12:47:01,680 Created temporary directory: /tmp/pip-unpack-lglssm6n 2022-12-01T12:47:01,680 Building wheels for collected packages: whatshap 2022-12-01T12:47:01,685 Created temporary directory: /tmp/pip-wheel-lz6v94t1 2022-12-01T12:47:01,685 Destination directory: /tmp/pip-wheel-lz6v94t1 2022-12-01T12:47:01,688 Building wheel for whatshap (pyproject.toml): started 2022-12-01T12:47:01,689 Running command Building wheel for whatshap (pyproject.toml) 2022-12-01T12:47:03,336 running bdist_wheel 2022-12-01T12:47:03,357 running build 2022-12-01T12:47:03,357 running build_py 2022-12-01T12:47:03,367 creating build 2022-12-01T12:47:03,367 creating build/lib.linux-armv7l-cpython-39 2022-12-01T12:47:03,368 creating build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,369 copying whatshap/_version.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,371 copying whatshap/variants.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,374 copying whatshap/timer.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,376 copying whatshap/__init__.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,378 copying whatshap/vcf.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,381 copying whatshap/__main__.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,383 copying whatshap/graph.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,385 copying whatshap/args.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,387 copying whatshap/variant.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,388 copying whatshap/verification.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,390 copying whatshap/merge.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,405 copying whatshap/utils.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,407 copying whatshap/bam.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,410 copying whatshap/testhelpers.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,412 copying whatshap/pedigree.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,415 copying whatshap/coverage.py -> build/lib.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,417 creating build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,418 copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,421 copying whatshap/cli/phase.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,424 copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,426 copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,429 copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,431 copying whatshap/cli/split.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,434 copying whatshap/cli/stats.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,436 copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,439 copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,442 copying whatshap/cli/polyphasegenetic.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,445 copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,447 copying whatshap/cli/compare.py -> build/lib.linux-armv7l-cpython-39/whatshap/cli 2022-12-01T12:47:03,451 creating build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,452 copying whatshap/polyphase/plots.py -> build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,455 copying whatshap/polyphase/__init__.py -> build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,457 copying whatshap/polyphase/threading.py -> build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,460 copying whatshap/polyphase/clusterarrangement.py -> build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,462 copying whatshap/polyphase/variantselection.py -> build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,464 copying whatshap/polyphase/algorithm.py -> build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,466 copying whatshap/polyphase/offspringscoring.py -> build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,469 copying whatshap/polyphase/reorder.py -> build/lib.linux-armv7l-cpython-39/whatshap/polyphase 2022-12-01T12:47:03,474 running build_ext 2022-12-01T12:47:03,480 building 'whatshap.core' extension 2022-12-01T12:47:03,531 creating build/temp.linux-armv7l-cpython-39 2022-12-01T12:47:03,532 creating build/temp.linux-armv7l-cpython-39/src 2022-12-01T12:47:03,533 creating build/temp.linux-armv7l-cpython-39/src/hapchat 2022-12-01T12:47:03,535 creating build/temp.linux-armv7l-cpython-39/whatshap 2022-12-01T12:47:03,536 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/backwardcolumniterator.cpp -o build/temp.linux-armv7l-cpython-39/src/backwardcolumniterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:05,184 In file included from /usr/include/c++/10/cassert:44, 2022-12-01T12:47:05,184 from src/backwardcolumniterator.cpp:1: 2022-12-01T12:47:05,185 src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’: 2022-12-01T12:47:05,185 src/backwardcolumniterator.cpp:121:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-12-01T12:47:05,185 121 | assert(k < positions->size()); 2022-12-01T12:47:05,185 | ~~^~~~~~~~~~~~~~~~~~~ 2022-12-01T12:47:05,185 src/backwardcolumniterator.cpp:140:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-12-01T12:47:05,186 140 | assert(active_entry < read->getVariantCount()); 2022-12-01T12:47:05,186 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-01T12:47:06,757 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/binomial.cpp -o build/temp.linux-armv7l-cpython-39/src/binomial.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:07,039 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/columnindexingiterator.cpp -o build/temp.linux-armv7l-cpython-39/src/columnindexingiterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:08,125 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2022-12-01T12:47:08,125 src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-12-01T12:47:08,125 90 | for(int j=0; j< parent->read_ids.size(); ++j) { 2022-12-01T12:47:08,125 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-01T12:47:08,126 src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:08,126 92 | if(m != -1) { 2022-12-01T12:47:08,126 | ~~^~~~~ 2022-12-01T12:47:08,126 src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable] 2022-12-01T12:47:08,126 89 | unsigned int s = 1; 2022-12-01T12:47:08,127 | ^ 2022-12-01T12:47:08,412 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/columnindexingscheme.cpp -o build/temp.linux-armv7l-cpython-39/src/columnindexingscheme.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:09,486 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2022-12-01T12:47:09,487 src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-12-01T12:47:09,487 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-12-01T12:47:09,487 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-12-01T12:47:09,490 71 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2022-12-01T12:47:09,490 71 | while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2022-12-01T12:47:11,570 src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-12-01T12:47:11,570 105 | assert(list_it->active_entry < read->getVariantCount()); 2022-12-01T12:47:11,570 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-01T12:47:11,587 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2022-12-01T12:47:11,588 src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-12-01T12:47:11,588 161 | assert(active_entry < read->getVariantCount()); 2022-12-01T12:47:11,588 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-01T12:47:13,226 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/entry.cpp -o build/temp.linux-armv7l-cpython-39/src/entry.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:14,204 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/genotype.cpp -o build/temp.linux-armv7l-cpython-39/src/genotype.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:16,494 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/genotypecolumncostcomputer.cpp -o build/temp.linux-armv7l-cpython-39/src/genotypecolumncostcomputer.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:19,248 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/genotypedistribution.cpp -o build/temp.linux-armv7l-cpython-39/src/genotypedistribution.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:20,421 src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’: 2022-12-01T12:47:20,421 src/genotypedistribution.cpp:55:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-12-01T12:47:20,421 55 | if (i == best_index) continue; 2022-12-01T12:47:20,422 | ~~^~~~~~~~~~~~~ 2022-12-01T12:47:20,882 In file included from /usr/include/c++/10/vector:72, 2022-12-01T12:47:20,883 from src/genotypedistribution.h:4, 2022-12-01T12:47:20,883 from src/genotypedistribution.cpp:5: 2022-12-01T12:47:20,883 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2022-12-01T12:47:20,883 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-12-01T12:47:20,884 426 | vector<_Tp, _Alloc>:: 2022-12-01T12:47:20,884 | ^~~~~~~~~~~~~~~~~~~ 2022-12-01T12:47:20,917 In file included from /usr/include/c++/10/vector:67, 2022-12-01T12:47:20,917 from src/genotypedistribution.h:4, 2022-12-01T12:47:20,917 from src/genotypedistribution.cpp:5: 2022-12-01T12:47:20,918 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’: 2022-12-01T12:47:20,918 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-12-01T12:47:20,918 1198 | _M_realloc_insert(end(), __x); 2022-12-01T12:47:20,918 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-12-01T12:47:20,918 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-12-01T12:47:20,918 1198 | _M_realloc_insert(end(), __x); 2022-12-01T12:47:20,918 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-12-01T12:47:20,919 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-12-01T12:47:20,919 1198 | _M_realloc_insert(end(), __x); 2022-12-01T12:47:20,919 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-12-01T12:47:21,103 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/genotypedptable.cpp -o build/temp.linux-armv7l-cpython-39/src/genotypedptable.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:23,189 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’: 2022-12-01T12:47:23,190 src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable] 2022-12-01T12:47:23,190 61 | size_t column_count = input_column_iterator.get_column_count(); 2022-12-01T12:47:23,190 | ^~~~~~~~~~~~ 2022-12-01T12:47:23,244 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’: 2022-12-01T12:47:23,245 src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable] 2022-12-01T12:47:23,245 91 | unsigned int transmission_configurations = pow(4, pedigree->triple_count()); 2022-12-01T12:47:23,245 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-01T12:47:23,248 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’: 2022-12-01T12:47:23,249 src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-12-01T12:47:23,249 152 | if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) { 2022-12-01T12:47:23,249 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-12-01T12:47:23,252 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’: 2022-12-01T12:47:23,252 src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable] 2022-12-01T12:47:23,252 178 | size_t k = (size_t)sqrt(input_column_iterator.get_column_count()); 2022-12-01T12:47:23,253 | ^ 2022-12-01T12:47:26,986 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/genotyper.cpp -o build/temp.linux-armv7l-cpython-39/src/genotyper.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:29,153 In file included from /usr/include/c++/10/vector:72, 2022-12-01T12:47:29,154 from src/columniterator.h:4, 2022-12-01T12:47:29,154 from src/genotyper.cpp:6: 2022-12-01T12:47:29,154 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Genotype&}; _Tp = Genotype; _Alloc = std::allocator]’: 2022-12-01T12:47:29,154 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-12-01T12:47:29,154 426 | vector<_Tp, _Alloc>:: 2022-12-01T12:47:29,154 | ^~~~~~~~~~~~~~~~~~~ 2022-12-01T12:47:29,349 In file included from /usr/include/c++/10/vector:67, 2022-12-01T12:47:29,349 from src/columniterator.h:4, 2022-12-01T12:47:29,349 from src/genotyper.cpp:6: 2022-12-01T12:47:29,349 /usr/include/c++/10/bits/stl_vector.h: In function ‘void compute_genotypes(const ReadSet&, std::vector*, std::vector*, std::vector*)’: 2022-12-01T12:47:29,350 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-12-01T12:47:29,350 1198 | _M_realloc_insert(end(), __x); 2022-12-01T12:47:29,350 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-12-01T12:47:29,734 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/graycodes.cpp -o build/temp.linux-armv7l-cpython-39/src/graycodes.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:30,756 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/hapchat/balancedcombinations.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/balancedcombinations.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:34,403 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/hapchat/basictypes.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/basictypes.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:36,016 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/hapchat/binomialcoefficient.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/binomialcoefficient.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:38,583 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/hapchat/hapchatcolumniterator.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/hapchatcolumniterator.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:40,849 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/hapchat/hapchatcore.cpp -o build/temp.linux-armv7l-cpython-39/src/hapchat/hapchatcore.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:42,999 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2022-12-01T12:47:42,999 src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2022-12-01T12:47:43,000 145 | Counter counter_columns; 2022-12-01T12:47:43,000 | ^~~~~~~~~~~~~~~ 2022-12-01T12:47:43,009 src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2022-12-01T12:47:43,010 src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:43,010 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2022-12-01T12:47:43,010 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:47:43,150 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2022-12-01T12:47:43,150 src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable] 2022-12-01T12:47:43,150 939 | int old_k = k_j[input_pointer]; 2022-12-01T12:47:43,150 | ^~~~~ 2022-12-01T12:47:43,168 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::intersect(const Column&, const Column&, const Pointer&, std::vector >&, std::vector >&, std::vector >&, std::vector&, const bool&)’: 2022-12-01T12:47:43,168 src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:43,168 1114 | (colJ[j].get_read_id() != -1) && 2022-12-01T12:47:43,169 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:47:43,169 src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:43,169 1115 | (colQ[i].get_read_id() != -1)) { 2022-12-01T12:47:43,169 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:47:43,171 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2022-12-01T12:47:43,171 src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:43,171 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2022-12-01T12:47:43,171 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:47:43,176 src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2022-12-01T12:47:43,176 src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:43,176 1294 | (colJ[j].get_read_id() != -1) && 2022-12-01T12:47:43,176 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:47:43,176 src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:43,177 1295 | (colQ[i].get_read_id() != -1)) { 2022-12-01T12:47:43,177 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:47:43,179 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::insert_col_and_update(std::vector >&, std::vector&, std::vector&, std::vector&, const Pointer&, const Column&, std::vector&, const Counter&)’: 2022-12-01T12:47:43,179 src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:43,179 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2022-12-01T12:47:43,180 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:47:44,214 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/indexset.cpp -o build/temp.linux-armv7l-cpython-39/src/indexset.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:45,770 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/multinomial.cpp -o build/temp.linux-armv7l-cpython-39/src/multinomial.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:46,983 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/pedigree.cpp -o build/temp.linux-armv7l-cpython-39/src/pedigree.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:48,359 In file included from /usr/include/c++/10/cassert:44, 2022-12-01T12:47:48,359 from src/pedigree.cpp:4: 2022-12-01T12:47:48,360 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2022-12-01T12:47:48,360 src/pedigree.cpp:32:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-12-01T12:47:48,360 32 | assert(genotypes.size() == variant_count); 2022-12-01T12:47:48,360 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-12-01T12:47:48,360 src/pedigree.cpp:33:37: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-12-01T12:47:48,360 33 | assert(genotype_likelihoods.size() == variant_count); 2022-12-01T12:47:48,361 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2022-12-01T12:47:48,370 src/pedigree.cpp: In member function ‘const Genotype* Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2022-12-01T12:47:48,370 src/pedigree.cpp:70:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2022-12-01T12:47:48,370 70 | assert(variant_index < variant_count); 2022-12-01T12:47:48,370 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2022-12-01T12:47:48,370 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2022-12-01T12:47:48,371 src/pedigree.cpp:81:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2022-12-01T12:47:48,371 81 | assert(variant_index < variant_count); 2022-12-01T12:47:48,371 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2022-12-01T12:47:48,382 src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’: 2022-12-01T12:47:48,383 src/pedigree.cpp:112:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2022-12-01T12:47:48,383 112 | for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2022-12-01T12:47:52,289 src/pedigreecolumncostcomputer.cpp:25:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:47:52,289 25 | for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2022-12-01T12:47:52,325 src/pedigreecolumncostcomputer.cpp:119:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2022-12-01T12:47:52,325 119 | unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2022-12-01T12:47:52,325 | ^~~~~~~~~~~~~~~~ 2022-12-01T12:47:53,449 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/pedigreedptable.cpp -o build/temp.linux-armv7l-cpython-39/src/pedigreedptable.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:47:59,634 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/pedigreepartitions.cpp -o build/temp.linux-armv7l-cpython-39/src/pedigreepartitions.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:48:01,520 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/phredgenotypelikelihoods.cpp -o build/temp.linux-armv7l-cpython-39/src/phredgenotypelikelihoods.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:48:03,095 In file included from /usr/include/c++/10/vector:72, 2022-12-01T12:48:03,095 from src/genotype.h:4, 2022-12-01T12:48:03,095 from src/phredgenotypelikelihoods.h:5, 2022-12-01T12:48:03,096 from src/phredgenotypelikelihoods.cpp:4: 2022-12-01T12:48:03,096 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’: 2022-12-01T12:48:03,096 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-12-01T12:48:03,096 426 | vector<_Tp, _Alloc>:: 2022-12-01T12:48:03,096 | ^~~~~~~~~~~~~~~~~~~ 2022-12-01T12:48:03,128 /usr/include/c++/10/bits/vector.tcc: In member function ‘void PhredGenotypeLikelihoods::get_genotypes(std::vector&) const’: 2022-12-01T12:48:03,128 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-12-01T12:48:03,128 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-12-01T12:48:03,129 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-01T12:48:03,282 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/read.cpp -o build/temp.linux-armv7l-cpython-39/src/read.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:48:06,269 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/readset.cpp -o build/temp.linux-armv7l-cpython-39/src/readset.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:48:10,791 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c src/transitionprobabilitycomputer.cpp -o build/temp.linux-armv7l-cpython-39/src/transitionprobabilitycomputer.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:48:13,274 In file included from /usr/include/c++/10/vector:72, 2022-12-01T12:48:13,274 from src/vector2d.h:5, 2022-12-01T12:48:13,274 from src/transitionprobabilitycomputer.h:5, 2022-12-01T12:48:13,275 from src/transitionprobabilitycomputer.cpp:1: 2022-12-01T12:48:13,275 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: 2022-12-01T12:48:13,275 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2022-12-01T12:48:13,275 426 | vector<_Tp, _Alloc>:: 2022-12-01T12:48:13,275 | ^~~~~~~~~~~~~~~~~~~ 2022-12-01T12:48:13,316 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Genotype&}; _Tp = Genotype; _Alloc = std::allocator]’: 2022-12-01T12:48:13,317 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-12-01T12:48:13,791 /usr/include/c++/10/bits/vector.tcc: In constructor ‘TransitionProbabilityComputer::TransitionProbabilityComputer(size_t, unsigned int, const Pedigree*, const std::vector&)’: 2022-12-01T12:48:13,792 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 2022-12-01T12:48:13,792 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-12-01T12:48:13,792 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-01T12:48:13,793 In file included from /usr/include/c++/10/vector:67, 2022-12-01T12:48:13,793 from src/vector2d.h:5, 2022-12-01T12:48:13,793 from src/transitionprobabilitycomputer.h:5, 2022-12-01T12:48:13,794 from src/transitionprobabilitycomputer.cpp:1: 2022-12-01T12:48:13,794 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-12-01T12:48:13,794 1198 | _M_realloc_insert(end(), __x); 2022-12-01T12:48:13,794 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-12-01T12:48:14,564 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNDEBUG -Isrc/ -I/usr/include/python3.9 -c whatshap/core.cpp -o build/temp.linux-armv7l-cpython-39/whatshap/core.o -std=c++11 -Werror=return-type -Werror=narrowing 2022-12-01T12:48:17,296 In file included from whatshap/core.cpp:843: 2022-12-01T12:48:17,296 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2022-12-01T12:48:17,296 src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2022-12-01T12:48:17,296 145 | Counter counter_columns; 2022-12-01T12:48:17,297 | ^~~~~~~~~~~~~~~ 2022-12-01T12:48:17,307 src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2022-12-01T12:48:17,308 src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:48:17,308 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2022-12-01T12:48:17,308 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:48:17,453 In file included from whatshap/core.cpp:843: 2022-12-01T12:48:17,453 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2022-12-01T12:48:17,453 src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable] 2022-12-01T12:48:17,453 939 | int old_k = k_j[input_pointer]; 2022-12-01T12:48:17,454 | ^~~~~ 2022-12-01T12:48:17,472 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::intersect(const Column&, const Column&, const Pointer&, std::vector >&, std::vector >&, std::vector >&, std::vector&, const bool&)’: 2022-12-01T12:48:17,472 src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:48:17,473 1114 | (colJ[j].get_read_id() != -1) && 2022-12-01T12:48:17,473 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:48:17,473 src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:48:17,473 1115 | (colQ[i].get_read_id() != -1)) { 2022-12-01T12:48:17,474 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:48:17,476 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2022-12-01T12:48:17,476 src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:48:17,476 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2022-12-01T12:48:17,476 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:48:17,481 src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2022-12-01T12:48:17,481 src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:48:17,481 1294 | (colJ[j].get_read_id() != -1) && 2022-12-01T12:48:17,481 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:48:17,481 src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:48:17,482 1295 | (colQ[i].get_read_id() != -1)) { 2022-12-01T12:48:17,482 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:48:17,484 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::insert_col_and_update(std::vector >&, std::vector&, std::vector&, std::vector&, const Pointer&, const Column&, std::vector&, const Counter&)’: 2022-12-01T12:48:17,484 src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-01T12:48:17,484 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2022-12-01T12:48:17,485 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2022-12-01T12:48:17,620 In file included from src/polyphase/haplothreader.h:4, 2022-12-01T12:48:17,620 from whatshap/core.cpp:849: 2022-12-01T12:48:17,620 src/polyphase/tuple.h: At global scope: 2022-12-01T12:48:17,621 src/polyphase/tuple.h:26:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,621 26 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2022-12-01T12:48:17,621 | ~~~~~^~~~~ 2022-12-01T12:48:17,621 src/polyphase/tuple.h:27:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,621 27 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2022-12-01T12:48:17,621 | ~~~~~^~~~~ 2022-12-01T12:48:17,621 src/polyphase/tuple.h:27:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,622 27 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2022-12-01T12:48:17,622 | ~~~~~^~~~~ 2022-12-01T12:48:17,622 src/polyphase/tuple.h:27:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,622 27 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2022-12-01T12:48:17,622 | ~~~~~^~~~~ 2022-12-01T12:48:17,622 src/polyphase/tuple.h:27:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,622 27 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2022-12-01T12:48:17,623 | ~~~~~^~~~~ 2022-12-01T12:48:17,623 src/polyphase/tuple.h:26:50: error: right operand of shift expression ‘(31 << 35)’ is greater than or equal to the precision 32 of the left operand [-fpermissive] 2022-12-01T12:48:17,623 26 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2022-12-01T12:48:17,623 | ~~~~~^~~~~ 2022-12-01T12:48:17,656 In file included from whatshap/core.cpp:850: 2022-12-01T12:48:17,656 src/polyphase/switchflipcalculator.h:31:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,657 31 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2022-12-01T12:48:17,657 | ~~~~~^~~~~ 2022-12-01T12:48:17,657 src/polyphase/switchflipcalculator.h:31:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,657 31 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2022-12-01T12:48:17,657 | ~~~~~^~~~~ 2022-12-01T12:48:17,657 src/polyphase/switchflipcalculator.h:31:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,657 31 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2022-12-01T12:48:17,658 | ~~~~~^~~~~ 2022-12-01T12:48:17,658 src/polyphase/switchflipcalculator.h:31:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,658 31 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2022-12-01T12:48:17,658 | ~~~~~^~~~~ 2022-12-01T12:48:17,658 src/polyphase/switchflipcalculator.h:32:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,658 32 | 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2022-12-01T12:48:17,658 | ~~~~~^~~~~ 2022-12-01T12:48:17,659 src/polyphase/switchflipcalculator.h:32:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,659 32 | 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2022-12-01T12:48:17,659 | ~~~~~^~~~~ 2022-12-01T12:48:17,659 src/polyphase/switchflipcalculator.h:32:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,659 32 | 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2022-12-01T12:48:17,659 | ~~~~~^~~~~ 2022-12-01T12:48:17,659 src/polyphase/switchflipcalculator.h:32:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2022-12-01T12:48:17,660 32 | 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2022-12-01T12:48:17,660 | ~~~~~^~~~~ 2022-12-01T12:48:17,660 src/polyphase/switchflipcalculator.h:31:14: error: right operand of shift expression ‘(15 << 32)’ is greater than or equal to the precision 32 of the left operand [-fpermissive] 2022-12-01T12:48:17,660 31 | 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2022-12-01T12:48:17,660 | ~~~~~^~~~~ 2022-12-01T12:48:17,953 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’: 2022-12-01T12:48:17,953 whatshap/core.cpp:8956:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2022-12-01T12:48:17,953 8956 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2022-12-01T12:48:17,954 | ~~~~~~~~~~^~~~~~~~~~~ 2022-12-01T12:48:18,215 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(__pyx_obj_8whatshap_4core_HapChatCore*)’: 2022-12-01T12:48:18,215 whatshap/core.cpp:15189:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2022-12-01T12:48:18,215 15189 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2022-12-01T12:48:18,216 | ~~~~~~~~~~^~~~~~~~~~~ 2022-12-01T12:48:20,154 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2022-12-01T12:48:20,341 ERROR: [present-rich] Building wheel for whatshap (pyproject.toml) exited with 1 2022-12-01T12:48:20,360 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/local/lib/python3.9/dist-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp0xwg2xqy[/] 2022-12-01T12:48:20,360 [bold magenta]cwd[/]: /tmp/pip-wheel-0uwx8eh3/whatshap_ad7b9343fa64467b840037bc2353ff2f 2022-12-01T12:48:20,360 Building wheel for whatshap (pyproject.toml): finished with status 'error' 2022-12-01T12:48:20,363 ERROR: Failed building wheel for whatshap 2022-12-01T12:48:20,365 Failed to build whatshap 2022-12-01T12:48:20,366 ERROR: Failed to build one or more wheels 2022-12-01T12:48:20,367 Exception information: 2022-12-01T12:48:20,367 Traceback (most recent call last): 2022-12-01T12:48:20,367 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 160, in exc_logging_wrapper 2022-12-01T12:48:20,367 status = run_func(*args) 2022-12-01T12:48:20,367 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 247, in wrapper 2022-12-01T12:48:20,367 return func(self, options, args) 2022-12-01T12:48:20,367 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 201, in run 2022-12-01T12:48:20,367 raise CommandError("Failed to build one or more wheels") 2022-12-01T12:48:20,367 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2022-12-01T12:48:20,371 Removed build tracker: '/tmp/pip-build-tracker-4bddtjsy'