2024-02-20T16:34:12,022 Created temporary directory: /tmp/pip-build-tracker-_isa4mha 2024-02-20T16:34:12,023 Initialized build tracking at /tmp/pip-build-tracker-_isa4mha 2024-02-20T16:34:12,023 Created build tracker: /tmp/pip-build-tracker-_isa4mha 2024-02-20T16:34:12,023 Entered build tracker: /tmp/pip-build-tracker-_isa4mha 2024-02-20T16:34:12,024 Created temporary directory: /tmp/pip-wheel-pt8v4tci 2024-02-20T16:34:12,029 Created temporary directory: /tmp/pip-ephem-wheel-cache-9yeovpkf 2024-02-20T16:34:12,055 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-02-20T16:34:12,059 2 location(s) to search for versions of pyfastani: 2024-02-20T16:34:12,059 * https://pypi.org/simple/pyfastani/ 2024-02-20T16:34:12,059 * https://www.piwheels.org/simple/pyfastani/ 2024-02-20T16:34:12,060 Fetching project page and analyzing links: https://pypi.org/simple/pyfastani/ 2024-02-20T16:34:12,060 Getting page https://pypi.org/simple/pyfastani/ 2024-02-20T16:34:12,062 Found index url https://pypi.org/simple/ 2024-02-20T16:34:12,124 Fetched page https://pypi.org/simple/pyfastani/ as application/vnd.pypi.simple.v1+json 2024-02-20T16:34:12,155 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/18/07/9ed2c77a83ae6bcce41fcfcf98969b25efc6b061ac740bb3bd70fd90de25/pyfastani-0.1.0-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,155 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/31/5a/fb8f4066ef68dd8eba0c289654cd5247244a01c6f6f9d0f91259c89a83f4/pyfastani-0.1.0-cp36-cp36m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,156 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/23/fb/c55d6b960314cb27f162ca010782906e0ccfe8390648cc01e82bab185953/pyfastani-0.1.0-cp37-cp37m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,156 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/7f/e4/6818f273e6990a0e649d236d44db7a3f56a694cbe6cba4b18fa51c517c4f/pyfastani-0.1.0-cp37-cp37m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,156 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/e0/7d/1efdab8fe5f1920cca5fb23d6506a5cb60bff0340b64d73f981466acf38e/pyfastani-0.1.0-cp38-cp38-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,156 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/a8/ea/0daaf8f35f62dcbad48bab59d26e6a811d93def44ebe1585d7c6fc289d0f/pyfastani-0.1.0-cp38-cp38-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,156 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/47/e9/3e6818ce5f4a58f82f4cc4181df9fe99a9626d2743beadfc4799a3961a8c/pyfastani-0.1.0-cp39-cp39-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,157 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/44/d6/d1c43c20d420c44f5944c0ff1b9527f7ad33a51f9263b98bd250a112eea9/pyfastani-0.1.0-cp39-cp39-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,157 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/46/54/84aedc9071fb3f9cc57c3ca1be666d5a2f4b194329ff35e3a496b99e0706/pyfastani-0.1.0-pp37-pypy37_pp73-macosx_10_7_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,157 Skipping link: No binaries permitted for pyfastani: 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https://files.pythonhosted.org/packages/be/8e/6b1c7e670bc230a51d1a05109d39d6d30d958561b3b9078e0cc4b48fac19/pyfastani-0.1.1.tar.gz (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6), version: 0.1.1 2024-02-20T16:34:12,161 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/a3/e8/88818abf7ba0a0c7e779c303153d463356ea8649c30cf73b075437dd8422/pyfastani-0.1.2-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,161 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/2a/ce/768ca2d25c107afb9f46bce03425dc46b6c26178465c3b4ab530e5960b84/pyfastani-0.1.2-cp36-cp36m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,161 Skipping link: No binaries permitted for pyfastani: 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https://files.pythonhosted.org/packages/92/e4/4cf543caa82eb48245cac9b1a7dfd40107d3fb0699f6fbbd1bc859b63cd4/pyfastani-0.5.1-pp310-pypy310_pp73-macosx_10_12_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,190 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/f8/19/ac3a7eba75e925be1bfb63a5d7217e43866176968b12285ededde6e51d6a/pyfastani-0.5.1-pp310-pypy310_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,190 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/ec/5a/0ffbd6388ac85afcdd176720ee185dd3af5bf58142a752947dbff5eb1785/pyfastani-0.5.1-pp310-pypy310_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,190 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/d8/f5/d027c5ba06de3a611ca35985d70cb37c2697db616ef8d27daa9f81b96235/pyfastani-0.5.1-pp37-pypy37_pp73-macosx_10_12_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,190 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/77/d5/ad24f075308eb655831bdb4829db83fd119156977c04b90345cfe33f4f09/pyfastani-0.5.1-pp37-pypy37_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,191 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/5d/16/01e43b7be3fa45c932788dd092b94e9daa531bcf90dc11133f6e6daee37e/pyfastani-0.5.1-pp37-pypy37_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,191 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/c6/28/35ebdde59e4c2cbbd335f895c69b3cf1cbd4fb20e529e7f708c6b3377d4d/pyfastani-0.5.1-pp38-pypy38_pp73-macosx_10_12_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,191 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/91/cb/b5352107728d1174bb8ffe217b60ebd52dad438c35104d42c9ae529abfe2/pyfastani-0.5.1-pp38-pypy38_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,191 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/45/af/c6bb77a8db331d8e26827d1d4d80156d4a70f7c6c7a765221d492d28b810/pyfastani-0.5.1-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,191 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/cb/81/36c3d22cf8cdfe9554c0f5a59979b1688c7a2fa9eb3731c27fc6bee62799/pyfastani-0.5.1-pp39-pypy39_pp73-macosx_10_12_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,192 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/2c/09/54739322efe3af2c1c523830f340790331ccd0c2e9a290ca12f7cb3aa81c/pyfastani-0.5.1-pp39-pypy39_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,192 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/2b/2a/ad98b9bfe6d3505cedfeab6316bfb1b8da6a5ab2bdb18a7fe65c13ae8616/pyfastani-0.5.1-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,192 Found link https://files.pythonhosted.org/packages/ef/e9/5684c4d334b11939e12c7f5acd00b5741017b859da0323e8a627cb1f9da9/pyfastani-0.5.1.tar.gz (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6), version: 0.5.1 2024-02-20T16:34:12,193 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyfastani/ 2024-02-20T16:34:12,193 Getting page https://www.piwheels.org/simple/pyfastani/ 2024-02-20T16:34:12,194 Found index url https://www.piwheels.org/simple/ 2024-02-20T16:34:12,282 Fetched page https://www.piwheels.org/simple/pyfastani/ as text/html 2024-02-20T16:34:12,288 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.5.1-cp311-cp311-linux_armv6l.whl#sha256=092d6613bcd1f309b1a33fa77a52276bb129afaf6a8db3265ea374d1333573a6 (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,288 Skipping link: No binaries permitted for pyfastani: 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https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.0-cp39-cp39-linux_armv7l.whl#sha256=7cbb59a8cfe273b488346a51698e3c64954d0273f25bfb12a209d0ef9aba7534 (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,291 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.0-cp311-cp311-linux_armv6l.whl#sha256=cb1e29cdc434665017f29f0a1c59540a70b1583a862cadf55db472bc7066ac9f (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,291 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.0-cp311-cp311-linux_armv7l.whl#sha256=cb1e29cdc434665017f29f0a1c59540a70b1583a862cadf55db472bc7066ac9f (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2024-02-20T16:34:12,291 Skipping link: not a file: https://www.piwheels.org/simple/pyfastani/ 2024-02-20T16:34:12,291 Skipping link: not a file: https://pypi.org/simple/pyfastani/ 2024-02-20T16:34:12,310 Given no hashes to check 1 links for project 'pyfastani': discarding no candidates 2024-02-20T16:34:12,327 Collecting pyfastani==0.5.1 2024-02-20T16:34:12,329 Created temporary directory: /tmp/pip-unpack-mabbjvr6 2024-02-20T16:34:12,378 Downloading pyfastani-0.5.1.tar.gz (4.6 MB) 2024-02-20T16:34:16,611 Added pyfastani==0.5.1 from https://files.pythonhosted.org/packages/ef/e9/5684c4d334b11939e12c7f5acd00b5741017b859da0323e8a627cb1f9da9/pyfastani-0.5.1.tar.gz to build tracker '/tmp/pip-build-tracker-_isa4mha' 2024-02-20T16:34:16,615 Created temporary directory: /tmp/pip-build-env-xm7eldcp 2024-02-20T16:34:16,626 Installing build dependencies: started 2024-02-20T16:34:16,627 Running command pip subprocess to install build dependencies 2024-02-20T16:34:18,620 Using pip 23.3 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2024-02-20T16:34:19,816 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-02-20T16:34:21,332 Collecting setuptools>=46.4 2024-02-20T16:34:21,348 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.1.0-py3-none-any.whl (819 kB) 2024-02-20T16:34:22,703 Collecting cython~=3.0 2024-02-20T16:34:22,705 Obtaining dependency information for cython~=3.0 from https://files.pythonhosted.org/packages/e3/7f/f584f5d15323feb897d42ef0e9d910649e2150d7a30cf7e7a8cc1d236e6f/Cython-3.0.8-py2.py3-none-any.whl.metadata 2024-02-20T16:34:22,713 Using cached Cython-3.0.8-py2.py3-none-any.whl.metadata (3.2 kB) 2024-02-20T16:34:22,888 Using cached Cython-3.0.8-py2.py3-none-any.whl (1.2 MB) 2024-02-20T16:34:25,703 Installing collected packages: setuptools, cython 2024-02-20T16:34:30,983 Creating /tmp/pip-build-env-xm7eldcp/overlay/bin 2024-02-20T16:34:30,985 changing mode of /tmp/pip-build-env-xm7eldcp/overlay/bin/cygdb to 755 2024-02-20T16:34:30,987 changing mode of /tmp/pip-build-env-xm7eldcp/overlay/bin/cython to 755 2024-02-20T16:34:30,989 changing mode of /tmp/pip-build-env-xm7eldcp/overlay/bin/cythonize to 755 2024-02-20T16:34:31,011 Successfully installed cython-3.0.8 setuptools-69.1.0 2024-02-20T16:34:31,194 WARNING: There was an error checking the latest version of pip. 2024-02-20T16:34:31,558 Installing build dependencies: finished with status 'done' 2024-02-20T16:34:31,563 Getting requirements to build wheel: started 2024-02-20T16:34:31,564 Running command Getting requirements to build wheel 2024-02-20T16:34:32,500 Getting requirements to build wheel: finished with status 'done' 2024-02-20T16:34:32,514 Installing backend dependencies: started 2024-02-20T16:34:32,515 Running command pip subprocess to install backend dependencies 2024-02-20T16:34:33,704 Using pip 23.3 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2024-02-20T16:34:34,300 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-02-20T16:34:34,658 Collecting wheel 2024-02-20T16:34:34,673 Using cached https://www.piwheels.org/simple/wheel/wheel-0.42.0-py3-none-any.whl (65 kB) 2024-02-20T16:34:37,376 Installing collected packages: wheel 2024-02-20T16:34:37,593 Creating /tmp/pip-build-env-xm7eldcp/normal/bin 2024-02-20T16:34:37,595 changing mode of /tmp/pip-build-env-xm7eldcp/normal/bin/wheel to 755 2024-02-20T16:34:37,609 Successfully installed wheel-0.42.0 2024-02-20T16:34:37,788 WARNING: There was an error checking the latest version of pip. 2024-02-20T16:34:38,019 Installing backend dependencies: finished with status 'done' 2024-02-20T16:34:38,021 Created temporary directory: /tmp/pip-modern-metadata-epikhj4s 2024-02-20T16:34:38,025 Preparing metadata (pyproject.toml): started 2024-02-20T16:34:38,026 Running command Preparing metadata (pyproject.toml) 2024-02-20T16:34:38,908 running dist_info 2024-02-20T16:34:38,925 creating /tmp/pip-modern-metadata-epikhj4s/pyfastani.egg-info 2024-02-20T16:34:38,930 writing /tmp/pip-modern-metadata-epikhj4s/pyfastani.egg-info/PKG-INFO 2024-02-20T16:34:38,935 writing dependency_links to /tmp/pip-modern-metadata-epikhj4s/pyfastani.egg-info/dependency_links.txt 2024-02-20T16:34:38,938 writing top-level names to /tmp/pip-modern-metadata-epikhj4s/pyfastani.egg-info/top_level.txt 2024-02-20T16:34:38,939 writing manifest file '/tmp/pip-modern-metadata-epikhj4s/pyfastani.egg-info/SOURCES.txt' 2024-02-20T16:34:38,968 reading manifest file '/tmp/pip-modern-metadata-epikhj4s/pyfastani.egg-info/SOURCES.txt' 2024-02-20T16:34:38,971 reading manifest template 'MANIFEST.in' 2024-02-20T16:34:39,763 warning: no files found matching '*.ipp' under directory 'vendor/boost-math/include_private' 2024-02-20T16:34:39,895 warning: no previously-included files found matching 'pyfastani/_fastani.cpp' 2024-02-20T16:34:39,896 warning: no previously-included files found matching 'pyfastani/_fasta.c' 2024-02-20T16:34:39,905 adding license file 'COPYING' 2024-02-20T16:34:39,929 writing manifest file '/tmp/pip-modern-metadata-epikhj4s/pyfastani.egg-info/SOURCES.txt' 2024-02-20T16:34:39,932 creating '/tmp/pip-modern-metadata-epikhj4s/pyfastani-0.5.1.dist-info' 2024-02-20T16:34:40,124 Preparing metadata (pyproject.toml): finished with status 'done' 2024-02-20T16:34:40,132 Source in /tmp/pip-wheel-pt8v4tci/pyfastani_b57d8fcdbbd64093935975282d3b8b05 has version 0.5.1, which satisfies requirement pyfastani==0.5.1 from https://files.pythonhosted.org/packages/ef/e9/5684c4d334b11939e12c7f5acd00b5741017b859da0323e8a627cb1f9da9/pyfastani-0.5.1.tar.gz 2024-02-20T16:34:40,132 Removed pyfastani==0.5.1 from https://files.pythonhosted.org/packages/ef/e9/5684c4d334b11939e12c7f5acd00b5741017b859da0323e8a627cb1f9da9/pyfastani-0.5.1.tar.gz from build tracker '/tmp/pip-build-tracker-_isa4mha' 2024-02-20T16:34:40,139 Created temporary directory: /tmp/pip-unpack-9wceffh6 2024-02-20T16:34:40,140 Created temporary directory: /tmp/pip-unpack-27nfuz8z 2024-02-20T16:34:40,143 Building wheels for collected packages: pyfastani 2024-02-20T16:34:40,147 Created temporary directory: /tmp/pip-wheel-6y3rsezw 2024-02-20T16:34:40,147 Destination directory: /tmp/pip-wheel-6y3rsezw 2024-02-20T16:34:40,150 Building wheel for pyfastani (pyproject.toml): started 2024-02-20T16:34:40,151 Running command Building wheel for pyfastani (pyproject.toml) 2024-02-20T16:34:41,061 running bdist_wheel 2024-02-20T16:34:41,092 running build 2024-02-20T16:34:41,093 running build_py 2024-02-20T16:34:41,101 creating build 2024-02-20T16:34:41,102 creating build/lib.linux-armv7l-cpython-39 2024-02-20T16:34:41,102 creating build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,103 copying pyfastani/__init__.py -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,106 creating build/lib.linux-armv7l-cpython-39/pyfastani/tests 2024-02-20T16:34:41,106 copying pyfastani/tests/test_sketch.py -> build/lib.linux-armv7l-cpython-39/pyfastani/tests 2024-02-20T16:34:41,108 copying pyfastani/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/pyfastani/tests 2024-02-20T16:34:41,110 copying pyfastani/tests/test_ani.py -> build/lib.linux-armv7l-cpython-39/pyfastani/tests 2024-02-20T16:34:41,112 creating build/lib.linux-armv7l-cpython-39/pyfastani/tests/data 2024-02-20T16:34:41,113 copying pyfastani/tests/data/__init__.py -> build/lib.linux-armv7l-cpython-39/pyfastani/tests/data 2024-02-20T16:34:41,114 running egg_info 2024-02-20T16:34:41,118 writing pyfastani.egg-info/PKG-INFO 2024-02-20T16:34:41,122 writing dependency_links to pyfastani.egg-info/dependency_links.txt 2024-02-20T16:34:41,124 writing top-level names to pyfastani.egg-info/top_level.txt 2024-02-20T16:34:41,136 reading manifest file 'pyfastani.egg-info/SOURCES.txt' 2024-02-20T16:34:41,152 reading manifest template 'MANIFEST.in' 2024-02-20T16:34:41,560 warning: no files found matching '*.ipp' under directory 'vendor/boost-math/include_private' 2024-02-20T16:34:41,687 warning: no previously-included files found matching 'pyfastani/_fastani.cpp' 2024-02-20T16:34:41,689 warning: no previously-included files found matching 'pyfastani/_fasta.c' 2024-02-20T16:34:41,698 adding license file 'COPYING' 2024-02-20T16:34:41,732 writing manifest file 'pyfastani.egg-info/SOURCES.txt' 2024-02-20T16:34:41,737 /tmp/pip-build-env-xm7eldcp/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pyfastani._sequtils' is absent from the `packages` configuration. 2024-02-20T16:34:41,738 !! 2024-02-20T16:34:41,738 ******************************************************************************** 2024-02-20T16:34:41,738 ############################ 2024-02-20T16:34:41,738 # Package would be ignored # 2024-02-20T16:34:41,738 ############################ 2024-02-20T16:34:41,738 Python recognizes 'pyfastani._sequtils' as an importable package[^1], 2024-02-20T16:34:41,739 but it is absent from setuptools' `packages` configuration. 2024-02-20T16:34:41,739 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-20T16:34:41,739 package, please make sure that 'pyfastani._sequtils' is explicitly added 2024-02-20T16:34:41,739 to the `packages` configuration field. 2024-02-20T16:34:41,739 Alternatively, you can also rely on setuptools' discovery methods 2024-02-20T16:34:41,739 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-20T16:34:41,739 instead of `find_packages(...)`/`find:`). 2024-02-20T16:34:41,740 You can read more about "package discovery" on setuptools documentation page: 2024-02-20T16:34:41,740 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-20T16:34:41,740 If you don't want 'pyfastani._sequtils' to be distributed and are 2024-02-20T16:34:41,740 already explicitly excluding 'pyfastani._sequtils' via 2024-02-20T16:34:41,740 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-20T16:34:41,740 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-20T16:34:41,741 combination with a more fine grained `package-data` configuration. 2024-02-20T16:34:41,741 You can read more about "package data files" on setuptools documentation page: 2024-02-20T16:34:41,741 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-20T16:34:41,741 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-20T16:34:41,741 even if it does not contain any `.py` files. 2024-02-20T16:34:41,742 On the other hand, currently there is no concept of package data 2024-02-20T16:34:41,742 directory, all directories are treated like packages. 2024-02-20T16:34:41,742 ******************************************************************************** 2024-02-20T16:34:41,742 !! 2024-02-20T16:34:41,742 check.warn(importable) 2024-02-20T16:34:41,784 copying pyfastani/_atomic_vector.hpp -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,786 copying pyfastani/_atomic_vector.pxd -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,788 copying pyfastani/_fasta.pyx -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,790 copying pyfastani/_fastani.pyi -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,792 copying pyfastani/_fastani.pyx -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,796 copying pyfastani/_patch.pxi -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,798 copying pyfastani/_utils.cpp -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,800 copying pyfastani/_utils.hpp -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,802 copying pyfastani/_utils.pxd -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,804 copying pyfastani/omp.cpp -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,806 copying pyfastani/omp.h -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,808 copying pyfastani/py.typed -> build/lib.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:41,809 creating build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:41,810 copying pyfastani/_sequtils/__init__.pxd -> build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:41,812 copying pyfastani/_sequtils/complement.h -> build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:41,814 copying pyfastani/_sequtils/neon.c -> build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:41,815 copying pyfastani/_sequtils/sequtils.cpp -> build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:41,817 copying pyfastani/_sequtils/sequtils.h -> build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:41,819 copying pyfastani/_sequtils/sse2.c -> build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:41,821 copying pyfastani/_sequtils/ssse3.c -> build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:41,823 copying pyfastani/tests/requirements.txt -> build/lib.linux-armv7l-cpython-39/pyfastani/tests 2024-02-20T16:34:41,825 copying pyfastani/tests/data/BGC0001425.faa -> build/lib.linux-armv7l-cpython-39/pyfastani/tests/data 2024-02-20T16:34:41,828 copying pyfastani/tests/data/BGC0001427.faa -> build/lib.linux-armv7l-cpython-39/pyfastani/tests/data 2024-02-20T16:34:41,831 copying pyfastani/tests/data/BGC0001428.faa -> build/lib.linux-armv7l-cpython-39/pyfastani/tests/data 2024-02-20T16:34:41,834 copying pyfastani/tests/data/Escherichia_coli_str_K12_MG1655.fna -> build/lib.linux-armv7l-cpython-39/pyfastani/tests/data 2024-02-20T16:34:41,933 copying pyfastani/tests/data/Shigella_flexneri_2a_01.fna -> build/lib.linux-armv7l-cpython-39/pyfastani/tests/data 2024-02-20T16:34:42,071 running build_clib 2024-02-20T16:34:42,075 creating build/temp.linux-armv7l-cpython-39 2024-02-20T16:34:42,076 generating build/temp.linux-armv7l-cpython-39/libcpu_features.a from vendor/cpu_features/src/filesystem.c, vendor/cpu_features/src/stack_line_reader.c, vendor/cpu_features/src/string_view.c, vendor/cpu_features/src/cpuinfo_aarch64.c, vendor/cpu_features/src/cpuinfo_arm.c, vendor/cpu_features/src/cpuinfo_x86.c 2024-02-20T16:34:42,078 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 -g -c build/temp.linux-armv7l-cpython-39/test_dlopen.c -o build/temp.linux-armv7l-cpython-39/test_dlopen.o 2024-02-20T16:34:42,163 found `dlopen` function from 2024-02-20T16:34:42,165 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 -g -c build/temp.linux-armv7l-cpython-39/test_getauxval.c -o build/temp.linux-armv7l-cpython-39/test_getauxval.o 2024-02-20T16:34:42,207 build/temp.linux-armv7l-cpython-39/test_getauxval.c:2:26: fatal error: sys/getauxval.h: No such file or directory 2024-02-20T16:34:42,207 2 | #include 2024-02-20T16:34:42,208 | ^~~~~~~~~~~~~~~~~ 2024-02-20T16:34:42,208 compilation terminated. 2024-02-20T16:34:42,210 could not find `getauxval` function from 2024-02-20T16:34:42,211 creating build/temp.linux-armv7l-cpython-39/vendor 2024-02-20T16:34:42,212 creating build/temp.linux-armv7l-cpython-39/vendor/cpu_features 2024-02-20T16:34:42,212 creating build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src 2024-02-20T16:34:42,213 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c vendor/cpu_features/src/cpuinfo_aarch64.c -o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/cpuinfo_aarch64.o 2024-02-20T16:34:42,258 In file included from vendor/cpu_features/src/cpuinfo_aarch64.c:15: 2024-02-20T16:34:42,259 vendor/cpu_features/include/cpuinfo_aarch64.h:153:2: error: #error "Including cpuinfo_aarch64.h from a non-aarch64 target." 2024-02-20T16:34:42,259 153 | #error "Including cpuinfo_aarch64.h from a non-aarch64 target." 2024-02-20T16:34:42,259 | ^~~~~ 2024-02-20T16:34:42,306 failed to compile platform-specific AARCH64 code 2024-02-20T16:34:42,307 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c vendor/cpu_features/src/cpuinfo_arm.c -o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/cpuinfo_arm.o 2024-02-20T16:34:42,825 successfully built platform-specific ARM code 2024-02-20T16:34:42,826 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c vendor/cpu_features/src/cpuinfo_x86.c -o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/cpuinfo_x86.o 2024-02-20T16:34:42,871 In file included from vendor/cpu_features/src/cpuinfo_x86.c:16: 2024-02-20T16:34:42,871 vendor/cpu_features/include/cpuinfo_x86.h:228:2: error: #error "Including cpuinfo_x86.h from a non-x86 target." 2024-02-20T16:34:42,871 228 | #error "Including cpuinfo_x86.h from a non-x86 target." 2024-02-20T16:34:42,871 | ^~~~~ 2024-02-20T16:34:42,887 vendor/cpu_features/src/cpuinfo_x86.c:25:2: error: #error "Cannot compile cpuinfo_x86 on a non x86 platform." 2024-02-20T16:34:42,888 25 | #error "Cannot compile cpuinfo_x86 on a non x86 platform." 2024-02-20T16:34:42,888 | ^~~~~ 2024-02-20T16:34:42,899 vendor/cpu_features/src/cpuinfo_x86.c:121:10: fatal error: cpuid.h: No such file or directory 2024-02-20T16:34:42,900 121 | #include 2024-02-20T16:34:42,900 | ^~~~~~~~~ 2024-02-20T16:34:42,900 compilation terminated. 2024-02-20T16:34:42,903 failed to compile platform-specific X86 code 2024-02-20T16:34:42,904 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c vendor/cpu_features/src/filesystem.c -o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/filesystem.o 2024-02-20T16:34:43,056 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c vendor/cpu_features/src/stack_line_reader.c -o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/stack_line_reader.o 2024-02-20T16:34:43,239 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c vendor/cpu_features/src/string_view.c -o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/string_view.o 2024-02-20T16:34:43,576 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 -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c vendor/cpu_features/src/hwcaps.c -o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/hwcaps.o 2024-02-20T16:34:43,765 arm-linux-gnueabihf-gcc-ar rcs build/temp.linux-armv7l-cpython-39/libcpu_features.a build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/filesystem.o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/stack_line_reader.o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/string_view.o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/hwcaps.o build/temp.linux-armv7l-cpython-39/vendor/cpu_features/src/cpuinfo_arm.o 2024-02-20T16:34:43,794 generating build/temp.linux-armv7l-cpython-39/libsequtils.a from pyfastani/_sequtils/sequtils.cpp, pyfastani/_sequtils/neon.c, pyfastani/_sequtils/sse2.c, pyfastani/_sequtils/ssse3.c 2024-02-20T16:34:43,795 creating build/temp.linux-armv7l-cpython-39/pyfastani 2024-02-20T16:34:43,795 creating build/temp.linux-armv7l-cpython-39/pyfastani/_sequtils 2024-02-20T16:34:43,796 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 -mfpu=neon -DARM_BUILD_SUPPORTED -Ipyfastani/_sequtils -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c pyfastani/_sequtils/neon.c -o build/temp.linux-armv7l-cpython-39/pyfastani/_sequtils/neon.o 2024-02-20T16:34:43,860 pyfastani/_sequtils/neon.c:2:10: fatal error: x86intrin.h: No such file or directory 2024-02-20T16:34:43,861 2 | #include 2024-02-20T16:34:43,861 | ^~~~~~~~~~~~~ 2024-02-20T16:34:43,861 compilation terminated. 2024-02-20T16:34:43,866 failed to compile platform-specific NEON code 2024-02-20T16:34:43,867 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 -msse2 -DARM_BUILD_SUPPORTED -Ipyfastani/_sequtils -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c pyfastani/_sequtils/sse2.c -o build/temp.linux-armv7l-cpython-39/pyfastani/_sequtils/sse2.o 2024-02-20T16:34:43,886 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’ 2024-02-20T16:34:43,887 failed to compile platform-specific SSE2 code 2024-02-20T16:34:43,889 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 -mssse3 -DARM_BUILD_SUPPORTED -Ipyfastani/_sequtils -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c pyfastani/_sequtils/ssse3.c -o build/temp.linux-armv7l-cpython-39/pyfastani/_sequtils/ssse3.o 2024-02-20T16:34:43,909 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-mssse3’ 2024-02-20T16:34:43,911 failed to compile platform-specific SSSE3 code 2024-02-20T16:34:43,912 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 -DARM_BUILD_SUPPORTED -Ipyfastani/_sequtils -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-39 -c pyfastani/_sequtils/sequtils.cpp -o build/temp.linux-armv7l-cpython-39/pyfastani/_sequtils/sequtils.o 2024-02-20T16:34:44,154 arm-linux-gnueabihf-gcc-ar rcs build/temp.linux-armv7l-cpython-39/libsequtils.a build/temp.linux-armv7l-cpython-39/pyfastani/_sequtils/sequtils.o 2024-02-20T16:34:44,171 running build_ext 2024-02-20T16:34:44,173 generating build/temp.linux-armv7l-cpython-39/cgi/include/computeCoreIdentity.hpp from vendor/FastANI/src/cgi/include/computeCoreIdentity.hpp 2024-02-20T16:34:44,173 creating build/temp.linux-armv7l-cpython-39/cgi 2024-02-20T16:34:44,173 creating build/temp.linux-armv7l-cpython-39/cgi/include 2024-02-20T16:34:44,179 generating build/temp.linux-armv7l-cpython-39/cgi/include/cgid_types.hpp from vendor/FastANI/src/cgi/include/cgid_types.hpp 2024-02-20T16:34:44,183 generating build/temp.linux-armv7l-cpython-39/map/include/winSketch.hpp from vendor/FastANI/src/map/include/winSketch.hpp 2024-02-20T16:34:44,183 creating build/temp.linux-armv7l-cpython-39/map 2024-02-20T16:34:44,184 creating build/temp.linux-armv7l-cpython-39/map/include 2024-02-20T16:34:44,188 generating build/temp.linux-armv7l-cpython-39/map/include/slidingMap.hpp from vendor/FastANI/src/map/include/slidingMap.hpp 2024-02-20T16:34:44,191 generating build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp from vendor/FastANI/src/map/include/computeMap.hpp 2024-02-20T16:34:44,194 generating build/temp.linux-armv7l-cpython-39/map/include/commonFunc.hpp from vendor/FastANI/src/map/include/commonFunc.hpp 2024-02-20T16:34:44,197 generating build/temp.linux-armv7l-cpython-39/map/include/MIIteratorL2.hpp from vendor/FastANI/src/map/include/MIIteratorL2.hpp 2024-02-20T16:34:44,199 generating build/temp.linux-armv7l-cpython-39/map/include/map_parameters.hpp from vendor/FastANI/src/map/include/map_parameters.hpp 2024-02-20T16:34:44,200 generating build/temp.linux-armv7l-cpython-39/map/include/map_stats.hpp from vendor/FastANI/src/map/include/map_stats.hpp 2024-02-20T16:34:44,202 generating build/temp.linux-armv7l-cpython-39/map/include/base_types.hpp from vendor/FastANI/src/map/include/base_types.hpp 2024-02-20T16:34:44,204 generating build/temp.linux-armv7l-cpython-39/map/include/parseCmdArgs.hpp from vendor/FastANI/src/map/include/parseCmdArgs.hpp 2024-02-20T16:34:44,206 generating build/temp.linux-armv7l-cpython-39/common/memcpyLink.h from vendor/FastANI/src/common/memcpyLink.h 2024-02-20T16:34:44,207 creating build/temp.linux-armv7l-cpython-39/common 2024-02-20T16:34:44,209 generating build/temp.linux-armv7l-cpython-39/common/prettyprint.hpp from vendor/FastANI/src/common/prettyprint.hpp 2024-02-20T16:34:44,211 generating build/temp.linux-armv7l-cpython-39/common/kseq.h from vendor/FastANI/src/common/kseq.h 2024-02-20T16:34:44,214 generating build/temp.linux-armv7l-cpython-39/common/murmur3.h from vendor/FastANI/src/common/murmur3.h 2024-02-20T16:34:44,216 generating build/temp.linux-armv7l-cpython-39/common/clipp.h from vendor/FastANI/src/common/clipp.h 2024-02-20T16:35:02,295 performance hint: pyfastani/_fastani.pyx:984:34: Exception check after calling '_do_l1_mappings' will always require the GIL to be acquired. 2024-02-20T16:35:02,295 Possible solutions: 2024-02-20T16:35:02,295 1. Declare '_do_l1_mappings' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2024-02-20T16:35:02,296 2. Use an 'int' return type on '_do_l1_mappings' to allow an error code to be returned. 2024-02-20T16:35:03,081 Compiling pyfastani/_fastani.pyx because it changed. 2024-02-20T16:35:03,081 Compiling pyfastani/_fasta.pyx because it changed. 2024-02-20T16:35:03,081 [1/2] Cythonizing pyfastani/_fasta.pyx 2024-02-20T16:35:03,081 [2/2] Cythonizing pyfastani/_fastani.pyx 2024-02-20T16:35:03,081 checking whether `PyInterpreterState_GetID` is available 2024-02-20T16:35:03,084 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 -I/usr/include/python3.9 -c build/temp.linux-armv7l-cpython-39/have_getid.c -o build/temp.linux-armv7l-cpython-39/have_getid.o -Werror=implicit-function-declaration 2024-02-20T16:35:03,638 yes 2024-02-20T16:35:03,643 building 'pyfastani._fastani' extension 2024-02-20T16:35:03,644 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 -DUSE_BOOST=1 -DBOOST_NO_EXCEPTIONS=1 -DBOOST_IF_CONSTEXPR=if -DCYTHON_WITHOUT_ASSERTIONS=1 -DHAS_PYINTERPRETERSTATE_GETID=1 -Ipyfastani/_sequtils -Ipyfastani -Iinclude -Ivendor/cpu_features/include -Ivendor/boost-math/include -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c pyfastani/_fastani.cpp -o build/temp.linux-armv7l-cpython-39/pyfastani/_fastani.o -std=c++11 2024-02-20T16:35:08,719 In file included from build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp:25, 2024-02-20T16:35:08,720 from pyfastani/_fastani.cpp:1294: 2024-02-20T16:35:08,720 build/temp.linux-armv7l-cpython-39/map/include/MIIteratorL2.hpp: In constructor ‘skch::MIIteratorL2::MIIteratorL2(skch::MIIteratorL2::MIIter_t, skch::MIIteratorL2::MIIter_t, skch::offset_t)’: 2024-02-20T16:35:08,720 build/temp.linux-armv7l-cpython-39/map/include/MIIteratorL2.hpp:49:16: warning: ‘skch::MIIteratorL2::sw_end’ will be initialized after [-Wreorder] 2024-02-20T16:35:08,720 49 | MIIter_t sw_end; 2024-02-20T16:35:08,720 | ^~~~~~ 2024-02-20T16:35:08,720 build/temp.linux-armv7l-cpython-39/map/include/MIIteratorL2.hpp:40:16: warning: ‘skch::offset_t skch::MIIteratorL2::countMinimizerWindows’ [-Wreorder] 2024-02-20T16:35:08,721 40 | offset_t countMinimizerWindows; 2024-02-20T16:35:08,721 | ^~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:08,721 build/temp.linux-armv7l-cpython-39/map/include/MIIteratorL2.hpp:56:7: warning: when initialized here [-Wreorder] 2024-02-20T16:35:08,721 56 | MIIteratorL2( MIIter_t firstSuperWindowRangeStart, 2024-02-20T16:35:08,721 | ^~~~~~~~~~~~ 2024-02-20T16:35:08,834 In file included from pyfastani/_fastani.cpp:1295: 2024-02-20T16:35:08,834 build/temp.linux-armv7l-cpython-39/cgi/include/computeCoreIdentity.hpp: In function ‘void cgi::outputVisualizationFile(skch::Parameters&, std::vector&, skch::Map&, skch::Sketch&, uint64_t, std::string&)’: 2024-02-20T16:35:08,834 build/temp.linux-armv7l-cpython-39/cgi/include/computeCoreIdentity.hpp:116:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-02-20T16:35:08,835 116 | for(int i = 0; i < mapper.metadata.size(); i++) 2024-02-20T16:35:08,835 | ~~^~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:08,835 build/temp.linux-armv7l-cpython-39/cgi/include/computeCoreIdentity.hpp:124:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-02-20T16:35:08,835 124 | for(int i = 0; i < refSketch.metadata.size(); i++) 2024-02-20T16:35:08,835 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:08,982 build/temp.linux-armv7l-cpython-39/cgi/include/computeCoreIdentity.hpp: In function ‘void cgi::splitReferenceGenomes(skch::Parameters&, std::vector&)’: 2024-02-20T16:35:08,982 build/temp.linux-armv7l-cpython-39/cgi/include/computeCoreIdentity.hpp:465:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2024-02-20T16:35:08,983 465 | for (int j = 0; j < parameters.refSequences.size(); j++) 2024-02-20T16:35:08,983 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:09,136 pyfastani/_fastani.cpp: In function ‘int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(__pyx_memoryview_obj*, PyObject*, int, int)’: 2024-02-20T16:35:09,136 pyfastani/_fastani.cpp:9220:15: warning: unused variable ‘__pyx_t_4’ [-Wunused-variable] 2024-02-20T16:35:09,136 9220 | Py_intptr_t __pyx_t_4; 2024-02-20T16:35:09,136 | ^~~~~~~~~ 2024-02-20T16:35:09,136 pyfastani/_fastani.cpp:9221:10: warning: unused variable ‘__pyx_t_5’ [-Wunused-variable] 2024-02-20T16:35:09,137 9221 | size_t __pyx_t_5; 2024-02-20T16:35:09,137 | ^~~~~~~~~ 2024-02-20T16:35:09,585 pyfastani/_fastani.cpp: In function ‘PyObject* __pyx_pf_9pyfastani_8_fastani_6Sketch_20occurences_threshold___get__(__pyx_obj_9pyfastani_8_fastani_Sketch*)’: 2024-02-20T16:35:09,586 pyfastani/_fastani.cpp:25274:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-02-20T16:35:09,586 25274 | int __pyx_t_1; 2024-02-20T16:35:09,586 | ^~~~~~~~~ 2024-02-20T16:35:09,727 pyfastani/_fastani.cpp: In function ‘PyObject* __pyx_pf_9pyfastani_8_fastani_6Mapper_12lookup_index___get__(__pyx_obj_9pyfastani_8_fastani_Mapper*)’: 2024-02-20T16:35:09,727 pyfastani/_fastani.cpp:28260:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-02-20T16:35:09,727 28260 | int __pyx_t_1; 2024-02-20T16:35:09,727 | ^~~~~~~~~ 2024-02-20T16:35:09,741 pyfastani/_fastani.cpp: In function ‘void __pyx_f_9pyfastani_8_fastani_6Mapper__do_l1_mappings(skch::Map&, int, const void*, Py_ssize_t, skch::QueryMetaData >&, std::vector&)’: 2024-02-20T16:35:09,742 pyfastani/_fastani.cpp:28606:53: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-02-20T16:35:09,742 28606 | __pyx_t_1 = (__pyx_v_hit_position_list.size() < __pyx_v_map.refSketch.getFreqThreshold()); 2024-02-20T16:35:09,742 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:10,108 pyfastani/_fastani.cpp: In function ‘Py_ssize_t __pyx_pf_9pyfastani_8_fastani_14MinimizerIndex_6__len__(__pyx_obj_9pyfastani_8_fastani_MinimizerIndex*)’: 2024-02-20T16:35:10,108 pyfastani/_fastani.cpp:35932:7: warning: unused variable ‘__pyx_t_1’ [-Wunused-variable] 2024-02-20T16:35:10,108 35932 | int __pyx_t_1; 2024-02-20T16:35:10,109 | ^~~~~~~~~ 2024-02-20T16:35:11,097 In file included from pyfastani/_fastani.cpp:1294: 2024-02-20T16:35:11,097 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp: In instantiation of ‘void skch::Map::computeL1CandidateRegions(Q_Info&, Vec1&, int, Vec2&) [with Q_Info = skch::QueryMetaData >; Vec1 = std::vector; Vec2 = std::vector]’: 2024-02-20T16:35:11,097 pyfastani/_fastani.cpp:28678:121: required from here 2024-02-20T16:35:11,098 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp:328:66: warning: comparison of integer expressions of different signedness: ‘skch::offset_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-02-20T16:35:11,098 328 | if(it2->seqId == it->seqId && it2->wpos - it->wpos < Q.kseq->seq.l) 2024-02-20T16:35:11,098 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2024-02-20T16:35:11,162 In file included from build/temp.linux-armv7l-cpython-39/map/include/winSketch.hpp:19, 2024-02-20T16:35:11,162 from pyfastani/_fastani.cpp:1293: 2024-02-20T16:35:11,163 build/temp.linux-armv7l-cpython-39/map/include/commonFunc.hpp: In instantiation of ‘void skch::CommonFunc::makeUpperCase(KSEQ) [with KSEQ = kseq_t*]’: 2024-02-20T16:35:11,163 build/temp.linux-armv7l-cpython-39/map/include/commonFunc.hpp:104:22: required from ‘void skch::CommonFunc::addMinimizers(std::vector&, KSEQ, int, int, int, skch::seqno_t) [with T = skch::MinimizerInfo; KSEQ = kseq_t*; skch::seqno_t = int]’ 2024-02-20T16:35:11,163 build/temp.linux-armv7l-cpython-39/map/include/winSketch.hpp:155:138: required from here 2024-02-20T16:35:11,163 build/temp.linux-armv7l-cpython-39/map/include/commonFunc.hpp:59:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-02-20T16:35:11,163 59 | for ( int i = 0; i < kseq->seq.l; i++ ) 2024-02-20T16:35:11,163 | ~~^~~~~~~~~~~~~ 2024-02-20T16:35:11,213 In file included from pyfastani/_fastani.cpp:1294: 2024-02-20T16:35:11,214 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp: In instantiation of ‘void skch::Map::doL1Mapping(Q_Info&, Vec&) [with Q_Info = skch::QueryMetaData >; Vec = std::vector]’: 2024-02-20T16:35:11,214 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp:212:22: required from ‘void skch::Map::mapSingleQuerySeq(Q_Info&, skch::MappingResultsVector_t&, std::ofstream&) [with Q_Info = skch::QueryMetaData >; skch::MappingResultsVector_t = std::vector; std::ofstream = std::basic_ofstream]’ 2024-02-20T16:35:11,214 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp:177:57: required from here 2024-02-20T16:35:11,214 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp:289:41: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-02-20T16:35:11,214 289 | if(hitPositionList.size() < refSketch.getFreqThreshold()) 2024-02-20T16:35:11,214 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:11,215 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp:277:15: warning: unused variable ‘totalMinimizersPicked’ [-Wunused-variable] 2024-02-20T16:35:11,215 277 | int totalMinimizersPicked = 0; 2024-02-20T16:35:11,215 | ^~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:50,968 In file included from /usr/include/c++/10/vector:72, 2024-02-20T16:35:50,969 from pyfastani/_fastani.cpp:1282: 2024-02-20T16:35:50,969 /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 long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: 2024-02-20T16:35:50,969 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-02-20T16:35:50,969 426 | vector<_Tp, _Alloc>:: 2024-02-20T16:35:50,969 | ^~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:51,084 /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector __pyx_convert_vector_from_py_uint64_t(PyObject*)’: 2024-02-20T16:35:51,084 /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 2024-02-20T16:35:51,084 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-02-20T16:35:51,084 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:51,258 pyfastani/_fastani.cpp:6257:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2024-02-20T16:35:51,258 6257 | } 2024-02-20T16:35:51,259 | ^ 2024-02-20T16:35:51,421 pyfastani/_fastani.cpp: In function ‘int __pyx_f_9pyfastani_8_fastani_6Sketch__add_draft(__pyx_obj_9pyfastani_8_fastani_Sketch*, PyObject*, PyObject*)’: 2024-02-20T16:35:51,421 pyfastani/_fastani.cpp:25723:76: warning: ‘__pyx_v_data’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-02-20T16:35:51,421 25723 | __pyx_t_9 = __pyx_f_9pyfastani_8_fastani__add_minimizers_nucl(__pyx_v_self->_sk->minimizerIndex, __pyx_v_kind, __pyx_v_data, __pyx_v_slen, __pyx_v_param->kmerSize, __pyx_v_param->windowSize, __pyx_v_self->_counter); if (unlikely(__pyx_t_9 == ((int)1))) __PYX_ERR(0, 650, __pyx_L13_error) 2024-02-20T16:35:51,421 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:51,428 In file included from /usr/include/c++/10/vector:72, 2024-02-20T16:35:51,429 from pyfastani/_fastani.cpp:1282: 2024-02-20T16:35:51,429 /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 2024-02-20T16:35:51,429 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-02-20T16:35:51,429 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:35:58,484 pyfastani/_fastani.cpp: In function ‘PyObject* __pyx_f_9pyfastani_8_fastani_6Mapper__query_draft(__pyx_obj_9pyfastani_8_fastani_Mapper*, PyObject*, __pyx_opt_args_9pyfastani_8_fastani_6Mapper__query_draft*)’: 2024-02-20T16:35:58,485 pyfastani/_fastani.cpp:30271:48: warning: ‘__pyx_v_data’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-02-20T16:35:58,485 30271 | __pyx_t_5 = PyMemoryView_FromMemory(((char *)__pyx_v_data), (__pyx_v_slen * __pyx_cur_scope->__pyx_v_stride), PyBUF_READ); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1090, __pyx_L11_error) 2024-02-20T16:35:58,485 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-02-20T16:36:00,178 In file included from pyfastani/_fastani.cpp:1294: 2024-02-20T16:36:00,179 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp: In member function ‘void skch::Map::computeL2MappedRegions(Q_Info&, skch::Map::L1_candidateLocus_t&, skch::Map::L2_mapLocus_t&) [with Q_Info = skch::QueryMetaData >]’: 2024-02-20T16:36:00,179 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp:492:52: warning: ‘lastOptimalPos’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-02-20T16:36:00,179 492 | l2_out.meanOptimalPos = (beginOptimalPos + lastOptimalPos)/2; 2024-02-20T16:36:00,179 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2024-02-20T16:36:00,179 build/temp.linux-armv7l-cpython-39/map/include/computeMap.hpp:492:52: warning: ‘beginOptimalPos’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-02-20T16:36:03,839 In file included from pyfastani/_fastani.cpp:1285: 2024-02-20T16:36:03,839 build/temp.linux-armv7l-cpython-39/map/include/map_stats.hpp: In function ‘int skch::Stat::recommendedWindowSize(double, int, int, float, int, uint64_t)’: 2024-02-20T16:36:03,840 build/temp.linux-armv7l-cpython-39/map/include/map_stats.hpp:252:33: warning: ‘optimalSketchSize’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-02-20T16:36:03,840 252 | int w = 2.0 * lengthQuery/optimalSketchSize; 2024-02-20T16:36:03,840 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2024-02-20T16:36:12,488 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 -DUSE_BOOST=1 -DBOOST_NO_EXCEPTIONS=1 -DBOOST_IF_CONSTEXPR=if -DCYTHON_WITHOUT_ASSERTIONS=1 -DHAS_PYINTERPRETERSTATE_GETID=1 -Ipyfastani/_sequtils -Ipyfastani -Iinclude -Ivendor/cpu_features/include -Ivendor/boost-math/include -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c pyfastani/_utils.cpp -o build/temp.linux-armv7l-cpython-39/pyfastani/_utils.o -std=c++11 2024-02-20T16:36:14,914 In file included from build/temp.linux-armv7l-cpython-39/map/include/winSketch.hpp:19, 2024-02-20T16:36:14,915 from pyfastani/_utils.hpp:14, 2024-02-20T16:36:14,915 from pyfastani/_utils.cpp:2: 2024-02-20T16:36:14,915 build/temp.linux-armv7l-cpython-39/map/include/commonFunc.hpp: In instantiation of ‘void skch::CommonFunc::makeUpperCase(KSEQ) [with KSEQ = kseq_t*]’: 2024-02-20T16:36:14,915 build/temp.linux-armv7l-cpython-39/map/include/commonFunc.hpp:104:22: required from ‘void skch::CommonFunc::addMinimizers(std::vector&, KSEQ, int, int, int, skch::seqno_t) [with T = skch::MinimizerInfo; KSEQ = kseq_t*; skch::seqno_t = int]’ 2024-02-20T16:36:14,915 build/temp.linux-armv7l-cpython-39/map/include/winSketch.hpp:155:138: required from here 2024-02-20T16:36:14,916 build/temp.linux-armv7l-cpython-39/map/include/commonFunc.hpp:59:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-02-20T16:36:14,916 59 | for ( int i = 0; i < kseq->seq.l; i++ ) 2024-02-20T16:36:14,916 | ~~^~~~~~~~~~~~~ 2024-02-20T16:36:15,381 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 -DUSE_BOOST=1 -DBOOST_NO_EXCEPTIONS=1 -DBOOST_IF_CONSTEXPR=if -DCYTHON_WITHOUT_ASSERTIONS=1 -DHAS_PYINTERPRETERSTATE_GETID=1 -Ipyfastani/_sequtils -Ipyfastani -Iinclude -Ivendor/cpu_features/include -Ivendor/boost-math/include -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c pyfastani/omp.cpp -o build/temp.linux-armv7l-cpython-39/pyfastani/omp.o -std=c++11 2024-02-20T16:36:15,480 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/pyfastani/_fastani.o build/temp.linux-armv7l-cpython-39/pyfastani/_utils.o build/temp.linux-armv7l-cpython-39/pyfastani/omp.o build/temp.linux-armv7l-cpython-39/libsequtils.a -L/usr/lib -Lbuild/temp.linux-armv7l-cpython-39 -lsequtils -lcpu_features -lsequtils -o build/lib.linux-armv7l-cpython-39/pyfastani/_fastani.cpython-39-arm-linux-gnueabihf.so -std=c++11 2024-02-20T16:36:16,060 building 'pyfastani._fasta' extension 2024-02-20T16:36:16,061 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 -DCYTHON_WITHOUT_ASSERTIONS=1 -DHAS_PYINTERPRETERSTATE_GETID=1 -Ipyfastani/_sequtils -Iinclude -Ipyfastani -Ivendor/cpu_features/include -Ipyfastani/simd -Ibuild/temp.linux-armv7l-cpython-39 -I/usr/include/python3.9 -c pyfastani/_fasta.c -o build/temp.linux-armv7l-cpython-39/pyfastani/_fasta.o 2024-02-20T16:36:21,148 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/pyfastani/_fasta.o build/temp.linux-armv7l-cpython-39/libsequtils.a -L/usr/lib -Lbuild/temp.linux-armv7l-cpython-39 -lsequtils -lcpu_features -lsequtils -o build/lib.linux-armv7l-cpython-39/pyfastani/_fasta.cpython-39-arm-linux-gnueabihf.so 2024-02-20T16:36:21,320 installing to build/bdist.linux-armv7l/wheel 2024-02-20T16:36:21,320 running install 2024-02-20T16:36:21,347 running install_lib 2024-02-20T16:36:21,354 creating build/bdist.linux-armv7l 2024-02-20T16:36:21,355 creating build/bdist.linux-armv7l/wheel 2024-02-20T16:36:21,357 creating build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,358 creating build/bdist.linux-armv7l/wheel/pyfastani/tests 2024-02-20T16:36:21,359 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/test_sketch.py -> build/bdist.linux-armv7l/wheel/pyfastani/tests 2024-02-20T16:36:21,361 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyfastani/tests 2024-02-20T16:36:21,364 creating build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2024-02-20T16:36:21,364 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/data/BGC0001425.faa -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2024-02-20T16:36:21,367 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/data/Escherichia_coli_str_K12_MG1655.fna -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2024-02-20T16:36:21,472 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/data/__init__.py -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2024-02-20T16:36:21,474 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/data/BGC0001427.faa -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2024-02-20T16:36:21,477 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/data/Shigella_flexneri_2a_01.fna -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2024-02-20T16:36:21,594 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/data/BGC0001428.faa -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2024-02-20T16:36:21,597 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/requirements.txt -> build/bdist.linux-armv7l/wheel/pyfastani/tests 2024-02-20T16:36:21,599 copying build/lib.linux-armv7l-cpython-39/pyfastani/tests/test_ani.py -> build/bdist.linux-armv7l/wheel/pyfastani/tests 2024-02-20T16:36:21,602 copying build/lib.linux-armv7l-cpython-39/pyfastani/_fastani.pyx -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,605 copying build/lib.linux-armv7l-cpython-39/pyfastani/_utils.pxd -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,607 copying build/lib.linux-armv7l-cpython-39/pyfastani/_atomic_vector.pxd -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,609 copying build/lib.linux-armv7l-cpython-39/pyfastani/_patch.pxi -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,610 copying build/lib.linux-armv7l-cpython-39/pyfastani/_utils.cpp -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,612 copying build/lib.linux-armv7l-cpython-39/pyfastani/_atomic_vector.hpp -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,614 copying build/lib.linux-armv7l-cpython-39/pyfastani/_utils.hpp -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,616 copying build/lib.linux-armv7l-cpython-39/pyfastani/__init__.py -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,617 copying build/lib.linux-armv7l-cpython-39/pyfastani/_fastani.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,739 copying build/lib.linux-armv7l-cpython-39/pyfastani/py.typed -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,741 copying build/lib.linux-armv7l-cpython-39/pyfastani/_fasta.pyx -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,744 copying build/lib.linux-armv7l-cpython-39/pyfastani/_fastani.pyi -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,746 copying build/lib.linux-armv7l-cpython-39/pyfastani/_fasta.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,754 creating build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2024-02-20T16:36:21,755 copying build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils/sequtils.cpp -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2024-02-20T16:36:21,758 copying build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils/neon.c -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2024-02-20T16:36:21,760 copying build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils/sequtils.h -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2024-02-20T16:36:21,762 copying build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils/complement.h -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2024-02-20T16:36:21,765 copying build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils/ssse3.c -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2024-02-20T16:36:21,767 copying build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils/__init__.pxd -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2024-02-20T16:36:21,769 copying build/lib.linux-armv7l-cpython-39/pyfastani/_sequtils/sse2.c -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2024-02-20T16:36:21,771 copying build/lib.linux-armv7l-cpython-39/pyfastani/omp.h -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,773 copying build/lib.linux-armv7l-cpython-39/pyfastani/omp.cpp -> build/bdist.linux-armv7l/wheel/pyfastani 2024-02-20T16:36:21,776 running install_egg_info 2024-02-20T16:36:21,792 Copying pyfastani.egg-info to build/bdist.linux-armv7l/wheel/pyfastani-0.5.1-py3.9.egg-info 2024-02-20T16:36:21,809 running install_scripts 2024-02-20T16:36:21,857 creating build/bdist.linux-armv7l/wheel/pyfastani-0.5.1.dist-info/WHEEL 2024-02-20T16:36:21,860 creating '/tmp/pip-wheel-6y3rsezw/.tmp-jxpt3ter/pyfastani-0.5.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-02-20T16:36:21,864 adding 'pyfastani/__init__.py' 2024-02-20T16:36:21,865 adding 'pyfastani/_atomic_vector.hpp' 2024-02-20T16:36:21,867 adding 'pyfastani/_atomic_vector.pxd' 2024-02-20T16:36:21,946 adding 'pyfastani/_fasta.cpython-39-arm-linux-gnueabihf.so' 2024-02-20T16:36:21,950 adding 'pyfastani/_fasta.pyx' 2024-02-20T16:36:22,730 adding 'pyfastani/_fastani.cpython-39-arm-linux-gnueabihf.so' 2024-02-20T16:36:22,763 adding 'pyfastani/_fastani.pyi' 2024-02-20T16:36:22,769 adding 'pyfastani/_fastani.pyx' 2024-02-20T16:36:22,770 adding 'pyfastani/_patch.pxi' 2024-02-20T16:36:22,772 adding 'pyfastani/_utils.cpp' 2024-02-20T16:36:22,773 adding 'pyfastani/_utils.hpp' 2024-02-20T16:36:22,774 adding 'pyfastani/_utils.pxd' 2024-02-20T16:36:22,775 adding 'pyfastani/omp.cpp' 2024-02-20T16:36:22,776 adding 'pyfastani/omp.h' 2024-02-20T16:36:22,777 adding 'pyfastani/py.typed' 2024-02-20T16:36:22,779 adding 'pyfastani/_sequtils/__init__.pxd' 2024-02-20T16:36:22,780 adding 'pyfastani/_sequtils/complement.h' 2024-02-20T16:36:22,781 adding 'pyfastani/_sequtils/neon.c' 2024-02-20T16:36:22,783 adding 'pyfastani/_sequtils/sequtils.cpp' 2024-02-20T16:36:22,784 adding 'pyfastani/_sequtils/sequtils.h' 2024-02-20T16:36:22,785 adding 'pyfastani/_sequtils/sse2.c' 2024-02-20T16:36:22,786 adding 'pyfastani/_sequtils/ssse3.c' 2024-02-20T16:36:22,788 adding 'pyfastani/tests/__init__.py' 2024-02-20T16:36:22,789 adding 'pyfastani/tests/requirements.txt' 2024-02-20T16:36:22,791 adding 'pyfastani/tests/test_ani.py' 2024-02-20T16:36:22,792 adding 'pyfastani/tests/test_sketch.py' 2024-02-20T16:36:22,795 adding 'pyfastani/tests/data/BGC0001425.faa' 2024-02-20T16:36:22,798 adding 'pyfastani/tests/data/BGC0001427.faa' 2024-02-20T16:36:22,801 adding 'pyfastani/tests/data/BGC0001428.faa' 2024-02-20T16:36:25,290 adding 'pyfastani/tests/data/Escherichia_coli_str_K12_MG1655.fna' 2024-02-20T16:36:27,899 adding 'pyfastani/tests/data/Shigella_flexneri_2a_01.fna' 2024-02-20T16:36:27,931 adding 'pyfastani/tests/data/__init__.py' 2024-02-20T16:36:27,933 adding 'pyfastani-0.5.1.dist-info/COPYING' 2024-02-20T16:36:27,936 adding 'pyfastani-0.5.1.dist-info/METADATA' 2024-02-20T16:36:27,937 adding 'pyfastani-0.5.1.dist-info/WHEEL' 2024-02-20T16:36:27,939 adding 'pyfastani-0.5.1.dist-info/top_level.txt' 2024-02-20T16:36:27,940 adding 'pyfastani-0.5.1.dist-info/RECORD' 2024-02-20T16:36:28,154 removing build/bdist.linux-armv7l/wheel 2024-02-20T16:36:29,135 Building wheel for pyfastani (pyproject.toml): finished with status 'done' 2024-02-20T16:36:29,248 Created wheel for pyfastani: filename=pyfastani-0.5.1-cp39-cp39-linux_armv7l.whl size=4770993 sha256=7008d50cbbd7dda713e9cf4512e3e9594bd3e6ced0cebfd3ef4721418f6da6b8 2024-02-20T16:36:29,249 Stored in directory: /tmp/pip-ephem-wheel-cache-9yeovpkf/wheels/be/52/5b/8722117754654be11f070f1c54344158b68318f101eb26b636 2024-02-20T16:36:29,264 Successfully built pyfastani 2024-02-20T16:36:29,447 Removed build tracker: '/tmp/pip-build-tracker-_isa4mha'