2024-04-03T12:28:19,160 Created temporary directory: /tmp/pip-build-tracker-ulyt9xm7 2024-04-03T12:28:19,161 Initialized build tracking at /tmp/pip-build-tracker-ulyt9xm7 2024-04-03T12:28:19,161 Created build tracker: /tmp/pip-build-tracker-ulyt9xm7 2024-04-03T12:28:19,162 Entered build tracker: /tmp/pip-build-tracker-ulyt9xm7 2024-04-03T12:28:19,163 Created temporary directory: /tmp/pip-wheel-dflra8kl 2024-04-03T12:28:19,166 Created temporary directory: /tmp/pip-ephem-wheel-cache-by8t75lb 2024-04-03T12:28:19,189 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-04-03T12:28:19,192 2 location(s) to search for versions of dinopy: 2024-04-03T12:28:19,192 * https://pypi.org/simple/dinopy/ 2024-04-03T12:28:19,192 * https://www.piwheels.org/simple/dinopy/ 2024-04-03T12:28:19,193 Fetching project page and analyzing links: https://pypi.org/simple/dinopy/ 2024-04-03T12:28:19,194 Getting page https://pypi.org/simple/dinopy/ 2024-04-03T12:28:19,195 Found index url https://pypi.org/simple/ 2024-04-03T12:28:19,408 Fetched page https://pypi.org/simple/dinopy/ as application/vnd.pypi.simple.v1+json 2024-04-03T12:28:19,411 Found link https://files.pythonhosted.org/packages/f2/68/3a8455f98893040edd9da0d033724fe16d09283c0b84bdbf8057c2221666/dinopy-1.1.1.tar.gz (from https://pypi.org/simple/dinopy/), version: 1.1.1 2024-04-03T12:28:19,411 Found link https://files.pythonhosted.org/packages/24/f5/1afcb87668d5d7b93b2365e1fa65a1768b243b742e7d7223acaf2a1d2403/dinopy-1.2.0.tar.gz (from https://pypi.org/simple/dinopy/), version: 1.2.0 2024-04-03T12:28:19,412 Found link https://files.pythonhosted.org/packages/f8/7a/b8ffa56c2f3e68ce7326269596cde7bcfd928d80d4807f683a6f6362d00a/dinopy-1.2.1.tar.gz (from https://pypi.org/simple/dinopy/), version: 1.2.1 2024-04-03T12:28:19,412 Found link https://files.pythonhosted.org/packages/4b/f8/85977ab9cf64cbc4ba0b76287f81b9596951ef60b3c3e6aa2b306501b6ec/dinopy-2.0.0.tar.gz (from https://pypi.org/simple/dinopy/), version: 2.0.0 2024-04-03T12:28:19,413 Found link https://files.pythonhosted.org/packages/b8/b8/65b5a2831143fc004fd57fcd8fbde73f0a9af1963171c074c0461830fd69/dinopy-2.0.1.tar.gz (from https://pypi.org/simple/dinopy/), version: 2.0.1 2024-04-03T12:28:19,414 Found link https://files.pythonhosted.org/packages/09/8a/7a2945c6e6b780bc259724d184076d2cdde35f8175a18e32af940b2d5887/dinopy-2.0.2.tar.gz (from https://pypi.org/simple/dinopy/), version: 2.0.2 2024-04-03T12:28:19,415 Found link https://files.pythonhosted.org/packages/a6/19/a91e3d4a5d9312a3dfaba0ec9187db90468eb86ae1f22262391f93d19bf7/dinopy-2.0.3.tar.gz (from https://pypi.org/simple/dinopy/), version: 2.0.3 2024-04-03T12:28:19,415 Found link https://files.pythonhosted.org/packages/9b/c4/5673afac336e4030b41c543fd7302dc6de5d048a87391b22e6d910c16482/dinopy-2.1.0.tar.gz (from https://pypi.org/simple/dinopy/), version: 2.1.0 2024-04-03T12:28:19,416 Found link https://files.pythonhosted.org/packages/f0/ae/9192e91468e8e8a27172bcf242d01006732ec28de1616970e7f0fe05c28e/dinopy-2.2.0.tar.gz (from https://pypi.org/simple/dinopy/), version: 2.2.0 2024-04-03T12:28:19,417 Found link https://files.pythonhosted.org/packages/2f/6c/eb26221f3b28e05ceede15e02a31c6fb3762940d46ac5cd3b1f56951b59a/dinopy-2.2.1.tar.gz (from https://pypi.org/simple/dinopy/), version: 2.2.1 2024-04-03T12:28:19,418 Found link https://files.pythonhosted.org/packages/e3/fd/06182a3e21bd400c172ef973512a070968c039a0f18f41c54c933fcafef9/dinopy-3.0.0.tar.gz (from https://pypi.org/simple/dinopy/), version: 3.0.0 2024-04-03T12:28:19,419 Fetching project page and analyzing links: https://www.piwheels.org/simple/dinopy/ 2024-04-03T12:28:19,419 Getting page https://www.piwheels.org/simple/dinopy/ 2024-04-03T12:28:19,421 Found index url https://www.piwheels.org/simple/ 2024-04-03T12:28:19,683 Fetched page https://www.piwheels.org/simple/dinopy/ as text/html 2024-04-03T12:28:19,697 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.1-cp35-cp35m-linux_armv6l.whl#sha256=454918b847930443eab659b762945e12349d8f801f64a953556f093afc2d3624 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,697 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.1-cp35-cp35m-linux_armv7l.whl#sha256=454918b847930443eab659b762945e12349d8f801f64a953556f093afc2d3624 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,698 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.1-cp37-cp37m-linux_armv6l.whl#sha256=62fff8ab8f9ce970aa89b56ebaac068fb27b6d7de9a96368a41dfa5ba3e0ceda (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,699 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.1-cp37-cp37m-linux_armv7l.whl#sha256=62fff8ab8f9ce970aa89b56ebaac068fb27b6d7de9a96368a41dfa5ba3e0ceda (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,699 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.1-cp39-cp39-linux_armv6l.whl#sha256=c3f7cc441c7af80592fb471f513977f90d415180b7d70b4008fbf053ea672061 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,700 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.1-cp39-cp39-linux_armv7l.whl#sha256=c3f7cc441c7af80592fb471f513977f90d415180b7d70b4008fbf053ea672061 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,700 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.0-cp35-cp35m-linux_armv7l.whl#sha256=718a8ac3544e237e77f46c07bb2f1b83879a8b82985663b00c3ed01b33929926 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,701 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.0-cp35-cp35m-linux_armv6l.whl#sha256=718a8ac3544e237e77f46c07bb2f1b83879a8b82985663b00c3ed01b33929926 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,702 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.0-cp37-cp37m-linux_armv6l.whl#sha256=70e29115ef30fde1a145f6513bf19d29286cde8dc6cb96569e226b07d0896a9f (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,702 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.0-cp37-cp37m-linux_armv7l.whl#sha256=70e29115ef30fde1a145f6513bf19d29286cde8dc6cb96569e226b07d0896a9f (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,703 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.0-cp39-cp39-linux_armv6l.whl#sha256=2edae690d15878fd3ff6610ee3847d2e2676a56b3d0d2b3b12ca829f0d31bfe5 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,704 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.2.0-cp39-cp39-linux_armv7l.whl#sha256=2edae690d15878fd3ff6610ee3847d2e2676a56b3d0d2b3b12ca829f0d31bfe5 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,704 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.1.0-cp34-cp34m-linux_armv7l.whl#sha256=abb4a6d1de109838f5f3982a5dda9a556b0494c0635b122923375b0c13137941 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,705 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.1.0-cp34-cp34m-linux_armv6l.whl#sha256=abb4a6d1de109838f5f3982a5dda9a556b0494c0635b122923375b0c13137941 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,706 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.1.0-cp35-cp35m-linux_armv6l.whl#sha256=da902c83e3e97afb1469af29eadfd96d24e7263559a11126460c597c1cdc74b0 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,706 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.1.0-cp35-cp35m-linux_armv7l.whl#sha256=da902c83e3e97afb1469af29eadfd96d24e7263559a11126460c597c1cdc74b0 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,707 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.1.0-cp37-cp37m-linux_armv7l.whl#sha256=0f92e4d09369ea4e40c5299242150725f75c157413e26702bbd5f2bfbdb095db (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,708 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.1.0-cp37-cp37m-linux_armv6l.whl#sha256=0f92e4d09369ea4e40c5299242150725f75c157413e26702bbd5f2bfbdb095db (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,708 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.1.0-cp39-cp39-linux_armv6l.whl#sha256=96a84dbe6290f38db027409d8b4d2c8bd1629f6f05bd7090e673e152599374fa (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,709 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.1.0-cp39-cp39-linux_armv7l.whl#sha256=96a84dbe6290f38db027409d8b4d2c8bd1629f6f05bd7090e673e152599374fa (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,709 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.3-cp34-cp34m-linux_armv6l.whl#sha256=fae15a94f9160247762dd9b850ae41cc0fa0c30e46af40d9c75565f94c6e96db (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,710 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.3-cp34-cp34m-linux_armv7l.whl#sha256=fae15a94f9160247762dd9b850ae41cc0fa0c30e46af40d9c75565f94c6e96db (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,710 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.3-cp35-cp35m-linux_armv6l.whl#sha256=f2fd11ca1038f294091efa9967712c3ecc168a11365d3ec555050a113c4ecaee (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,711 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.3-cp35-cp35m-linux_armv7l.whl#sha256=f2fd11ca1038f294091efa9967712c3ecc168a11365d3ec555050a113c4ecaee (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,711 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.3-cp37-cp37m-linux_armv7l.whl#sha256=8fabc61b0a530825cb2788dbb1e550a45e89aef2046a45d54fd83ef5c598e0b3 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,712 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.3-cp37-cp37m-linux_armv6l.whl#sha256=8fabc61b0a530825cb2788dbb1e550a45e89aef2046a45d54fd83ef5c598e0b3 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,713 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.2-cp34-cp34m-linux_armv7l.whl#sha256=b95c573638f0211395dd980693380fd1448ded7dbdd3a5c9f9a4f18728156400 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,713 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.2-cp34-cp34m-linux_armv6l.whl#sha256=b95c573638f0211395dd980693380fd1448ded7dbdd3a5c9f9a4f18728156400 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,714 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.2-cp35-cp35m-linux_armv6l.whl#sha256=30d6340198b83fd7275374e709a65b5762c2a712cbb73e1b0bb82eb6949e593b (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,715 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.2-cp35-cp35m-linux_armv7l.whl#sha256=30d6340198b83fd7275374e709a65b5762c2a712cbb73e1b0bb82eb6949e593b (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,715 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.2-cp37-cp37m-linux_armv6l.whl#sha256=aea1c51d33808c182ae8a1e2d1ae88c5ee834cfb9265d0a712bdd9bc02c6472d (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,716 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.2-cp37-cp37m-linux_armv7l.whl#sha256=aea1c51d33808c182ae8a1e2d1ae88c5ee834cfb9265d0a712bdd9bc02c6472d (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,717 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.1-cp37-cp37m-linux_armv6l.whl#sha256=c5d5ecaaca2cbbf3792a5c6d852932b2730545fc1f2d19c5b1fa52ddb399a01b (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,718 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.1-cp37-cp37m-linux_armv7l.whl#sha256=c5d5ecaaca2cbbf3792a5c6d852932b2730545fc1f2d19c5b1fa52ddb399a01b (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,930 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-2.0.1-cp35-cp35m-linux_armv7l.whl#sha256=d14685a13c8cd08ca0ef815639cc48cb82572deef5e60c40fe33149ab5e1e4a9 (from 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https://www.piwheels.org/simple/dinopy/dinopy-1.1.1-cp34-cp34m-linux_armv6l.whl#sha256=22fe9172190e4cedaa3c33cbfab0500a1a391f23c367a1ea9b23824473a5d6e9 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,949 Skipping link: No binaries permitted for dinopy: https://www.piwheels.org/simple/dinopy/dinopy-1.1.1-cp34-cp34m-linux_armv7l.whl#sha256=22fe9172190e4cedaa3c33cbfab0500a1a391f23c367a1ea9b23824473a5d6e9 (from https://www.piwheels.org/simple/dinopy/) 2024-04-03T12:28:19,950 Skipping link: not a file: https://www.piwheels.org/simple/dinopy/ 2024-04-03T12:28:19,951 Skipping link: not a file: https://pypi.org/simple/dinopy/ 2024-04-03T12:28:19,999 Given no hashes to check 1 links for project 'dinopy': discarding no candidates 2024-04-03T12:28:20,027 Collecting dinopy==3.0.0 2024-04-03T12:28:20,030 Created temporary directory: /tmp/pip-unpack-0jw66ws_ 2024-04-03T12:28:20,167 Downloading dinopy-3.0.0.tar.gz (744 kB) 2024-04-03T12:28:20,843 Added dinopy==3.0.0 from https://files.pythonhosted.org/packages/e3/fd/06182a3e21bd400c172ef973512a070968c039a0f18f41c54c933fcafef9/dinopy-3.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-ulyt9xm7' 2024-04-03T12:28:20,850 Created temporary directory: /tmp/pip-build-env-_p7s8k1e 2024-04-03T12:28:20,855 Installing build dependencies: started 2024-04-03T12:28:20,856 Running command pip subprocess to install build dependencies 2024-04-03T12:28:22,000 Using pip 24.0 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-04-03T12:28:22,517 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-04-03T12:28:23,987 Collecting setuptools>=48.0 2024-04-03T12:28:24,002 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.2.0-py3-none-any.whl (821 kB) 2024-04-03T12:28:24,316 Collecting setuptools_scm 2024-04-03T12:28:24,334 Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-8.0.4-py3-none-any.whl (42 kB) 2024-04-03T12:28:24,534 Collecting wheel 2024-04-03T12:28:24,548 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-04-03T12:28:25,756 Collecting Cython>=3.0.0 2024-04-03T12:28:25,770 Using cached https://www.piwheels.org/simple/cython/Cython-3.0.10-cp311-cp311-linux_armv7l.whl (11.8 MB) 2024-04-03T12:28:27,205 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-04-03T12:28:27,209 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2024-04-03T12:28:27,213 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): 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2024-04-03T12:28:28,173 Using cached https://www.piwheels.org/simple/packaging/packaging-24.0-py3-none-any.whl (53 kB) 2024-04-03T12:28:28,292 Collecting typing-extensions (from setuptools_scm) 2024-04-03T12:28:28,307 Using cached https://www.piwheels.org/simple/typing-extensions/typing_extensions-4.10.0-py3-none-any.whl (33 kB) 2024-04-03T12:28:30,919 Installing collected packages: wheel, typing-extensions, setuptools, packaging, numpy, Cython, setuptools_scm 2024-04-03T12:28:31,153 Creating /tmp/pip-build-env-_p7s8k1e/overlay/local/bin 2024-04-03T12:28:31,156 changing mode of /tmp/pip-build-env-_p7s8k1e/overlay/local/bin/wheel to 755 2024-04-03T12:28:44,447 changing mode of /tmp/pip-build-env-_p7s8k1e/overlay/local/bin/f2py to 755 2024-04-03T12:28:49,344 changing mode of /tmp/pip-build-env-_p7s8k1e/overlay/local/bin/cygdb to 755 2024-04-03T12:28:49,346 changing mode of /tmp/pip-build-env-_p7s8k1e/overlay/local/bin/cython to 755 2024-04-03T12:28:49,348 changing mode of /tmp/pip-build-env-_p7s8k1e/overlay/local/bin/cythonize to 755 2024-04-03T12:28:49,834 Successfully installed Cython-3.0.10 numpy-1.26.4 packaging-24.0 setuptools-69.2.0 setuptools_scm-8.0.4 typing-extensions-4.10.0 wheel-0.43.0 2024-04-03T12:28:50,873 Installing build dependencies: finished with status 'done' 2024-04-03T12:28:50,876 Getting requirements to build wheel: started 2024-04-03T12:28:50,877 Running command Getting requirements to build wheel 2024-04-03T12:29:27,422 Compiling dinopy/auxiliary.pyx because it changed. 2024-04-03T12:29:27,423 Compiling dinopy/conversion.pyx because it changed. 2024-04-03T12:29:27,424 Compiling dinopy/creader.pyx because it changed. 2024-04-03T12:29:27,425 Compiling dinopy/definitions.pyx because it changed. 2024-04-03T12:29:27,426 Compiling dinopy/fasta_reader.pyx because it changed. 2024-04-03T12:29:27,427 Compiling dinopy/fasta_writer.pyx because it changed. 2024-04-03T12:29:27,427 Compiling dinopy/fastq_reader.pyx because it changed. 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Cythonizing dinopy/wrap_sais.pyx 2024-04-03T12:29:27,556 running egg_info 2024-04-03T12:29:27,563 writing dinopy.egg-info/PKG-INFO 2024-04-03T12:29:27,567 writing dependency_links to dinopy.egg-info/dependency_links.txt 2024-04-03T12:29:27,569 writing requirements to dinopy.egg-info/requires.txt 2024-04-03T12:29:27,570 writing top-level names to dinopy.egg-info/top_level.txt 2024-04-03T12:29:27,621 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,622 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,622 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in 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be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,643 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,643 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,644 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,644 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,645 dependency 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be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,648 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,648 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,649 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,649 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,650 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,650 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,651 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,652 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,652 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,653 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,653 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,654 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:27,668 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2024-04-03T12:29:27,672 reading manifest file 'dinopy.egg-info/SOURCES.txt' 2024-04-03T12:29:27,690 reading manifest template 'MANIFEST.in' 2024-04-03T12:29:27,691 adding license file 'LICENSE.rst' 2024-04-03T12:29:27,692 adding license file 'AUTHORS.rst' 2024-04-03T12:29:27,698 writing manifest file 'dinopy.egg-info/SOURCES.txt' 2024-04-03T12:29:28,502 Getting requirements to build wheel: finished with status 'done' 2024-04-03T12:29:28,516 Created temporary directory: /tmp/pip-modern-metadata-gouaqz5n 2024-04-03T12:29:28,519 Preparing metadata (pyproject.toml): started 2024-04-03T12:29:28,520 Running command Preparing metadata (pyproject.toml) 2024-04-03T12:29:31,354 running dist_info 2024-04-03T12:29:31,362 creating /tmp/pip-modern-metadata-gouaqz5n/dinopy.egg-info 2024-04-03T12:29:31,369 writing /tmp/pip-modern-metadata-gouaqz5n/dinopy.egg-info/PKG-INFO 2024-04-03T12:29:31,374 writing dependency_links to /tmp/pip-modern-metadata-gouaqz5n/dinopy.egg-info/dependency_links.txt 2024-04-03T12:29:31,376 writing requirements to /tmp/pip-modern-metadata-gouaqz5n/dinopy.egg-info/requires.txt 2024-04-03T12:29:31,377 writing top-level names to /tmp/pip-modern-metadata-gouaqz5n/dinopy.egg-info/top_level.txt 2024-04-03T12:29:31,378 writing manifest file '/tmp/pip-modern-metadata-gouaqz5n/dinopy.egg-info/SOURCES.txt' 2024-04-03T12:29:31,420 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,420 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,421 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,421 dependency 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be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,424 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,425 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,426 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,426 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,427 dependency 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be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,430 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,431 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,431 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,432 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,432 dependency 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be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,435 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,436 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,436 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,437 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,437 dependency 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/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,446 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,446 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,447 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,449 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,450 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,451 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,452 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,453 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,454 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,455 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,456 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,458 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,459 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,459 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,460 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,461 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,461 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,462 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,462 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,463 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:29:31,472 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2024-04-03T12:29:31,475 reading manifest file '/tmp/pip-modern-metadata-gouaqz5n/dinopy.egg-info/SOURCES.txt' 2024-04-03T12:29:31,478 reading manifest template 'MANIFEST.in' 2024-04-03T12:29:31,479 adding license file 'LICENSE.rst' 2024-04-03T12:29:31,480 adding license file 'AUTHORS.rst' 2024-04-03T12:29:31,483 writing manifest file '/tmp/pip-modern-metadata-gouaqz5n/dinopy.egg-info/SOURCES.txt' 2024-04-03T12:29:31,484 creating '/tmp/pip-modern-metadata-gouaqz5n/dinopy-3.0.0.dist-info' 2024-04-03T12:29:31,978 Preparing metadata (pyproject.toml): finished with status 'done' 2024-04-03T12:29:31,984 Source in /tmp/pip-wheel-dflra8kl/dinopy_34b477274cf44e0d9322af9c36e40f7a has version 3.0.0, which satisfies requirement dinopy==3.0.0 from https://files.pythonhosted.org/packages/e3/fd/06182a3e21bd400c172ef973512a070968c039a0f18f41c54c933fcafef9/dinopy-3.0.0.tar.gz 2024-04-03T12:29:31,985 Removed dinopy==3.0.0 from https://files.pythonhosted.org/packages/e3/fd/06182a3e21bd400c172ef973512a070968c039a0f18f41c54c933fcafef9/dinopy-3.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-ulyt9xm7' 2024-04-03T12:29:31,991 Created temporary directory: /tmp/pip-unpack-sl1ymhge 2024-04-03T12:29:31,992 Created temporary directory: /tmp/pip-unpack-rxx3jwg6 2024-04-03T12:29:32,000 Building wheels for collected packages: dinopy 2024-04-03T12:29:32,006 Created temporary directory: /tmp/pip-wheel-rn0r_01_ 2024-04-03T12:29:32,006 Destination directory: /tmp/pip-wheel-rn0r_01_ 2024-04-03T12:29:32,009 Building wheel for dinopy (pyproject.toml): started 2024-04-03T12:29:32,011 Running command Building wheel for dinopy (pyproject.toml) 2024-04-03T12:29:34,575 running bdist_wheel 2024-04-03T12:29:34,634 running build 2024-04-03T12:29:34,635 running build_py 2024-04-03T12:29:34,645 creating build 2024-04-03T12:29:34,645 creating build/lib.linux-armv7l-cpython-311 2024-04-03T12:29:34,646 creating build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,647 copying dinopy/exceptions.py -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,650 copying dinopy/__init__.py -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,652 copying dinopy/fai_io.py -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,660 copying dinopy/shaping.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,664 copying dinopy/fasta_reader.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,667 copying dinopy/output_opener.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,670 copying dinopy/sam_reader.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,673 copying dinopy/shape.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,675 copying dinopy/auxiliary.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,678 copying dinopy/fastq_reader.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,681 copying dinopy/fastq_writer.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,684 copying dinopy/sambam.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,688 copying dinopy/wrap_sais.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,690 copying dinopy/nameline_parser.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,693 copying dinopy/conversion.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,696 copying dinopy/sam_writer.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,699 copying dinopy/creader.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,702 copying dinopy/definitions.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,705 copying dinopy/fasta_writer.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,707 copying dinopy/input_opener.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,710 copying dinopy/processors.pyx -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,712 copying dinopy/__init__.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,714 copying dinopy/sambam.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,716 copying dinopy/sam_writer.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,718 copying dinopy/definitions.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,720 copying dinopy/auxiliary.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,722 copying dinopy/sam_reader.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,724 copying dinopy/processors.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,726 copying dinopy/fastq_reader.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,728 copying dinopy/conversion.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,730 copying dinopy/creader.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,731 copying dinopy/shaping.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,734 copying dinopy/output_opener.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,735 copying dinopy/wrap_sais.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,737 copying dinopy/shape.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,739 copying dinopy/fasta_reader.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,741 copying dinopy/nameline_parser.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,743 copying dinopy/fastq_writer.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,746 copying dinopy/fasta_writer.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,748 copying dinopy/input_opener.pxd -> build/lib.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,750 creating build/lib.linux-armv7l-cpython-311/dinopy/cpp 2024-04-03T12:29:34,751 copying dinopy/cpp/sais.cpp -> build/lib.linux-armv7l-cpython-311/dinopy/cpp 2024-04-03T12:29:34,754 copying dinopy/../README.rst -> build/lib.linux-armv7l-cpython-311/dinopy/.. 2024-04-03T12:29:34,757 running build_ext 2024-04-03T12:29:34,764 building 'dinopy.auxiliary' extension 2024-04-03T12:29:34,764 creating build/temp.linux-armv7l-cpython-311 2024-04-03T12:29:34,765 creating build/temp.linux-armv7l-cpython-311/dinopy 2024-04-03T12:29:34,766 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/auxiliary.c -o build/temp.linux-armv7l-cpython-311/dinopy/auxiliary.o -O3 2024-04-03T12:29:35,178 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:29:35,179 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:29:35,180 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:29:35,180 from dinopy/auxiliary.c:1252: 2024-04-03T12:29:35,181 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:29:35,181 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:29:35,182 | ^~~~~~~ 2024-04-03T12:29:44,490 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/auxiliary.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/auxiliary.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:29:44,670 building 'dinopy.conversion' extension 2024-04-03T12:29:44,671 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/conversion.c -o build/temp.linux-armv7l-cpython-311/dinopy/conversion.o -O3 2024-04-03T12:29:45,069 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:29:45,070 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:29:45,071 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:29:45,071 from dinopy/conversion.c:1269: 2024-04-03T12:29:45,072 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:29:45,072 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:29:45,073 | ^~~~~~~ 2024-04-03T12:30:07,764 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/conversion.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/conversion.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:30:07,917 building 'dinopy.creader' extension 2024-04-03T12:30:07,918 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/creader.c -o build/temp.linux-armv7l-cpython-311/dinopy/creader.o -O3 2024-04-03T12:30:23,977 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/creader.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/creader.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:30:24,104 building 'dinopy.definitions' extension 2024-04-03T12:30:24,106 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/definitions.c -o build/temp.linux-armv7l-cpython-311/dinopy/definitions.o -O3 2024-04-03T12:30:24,508 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:30:24,509 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:30:24,509 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:30:24,510 from dinopy/definitions.c:1269: 2024-04-03T12:30:24,510 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:30:24,511 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:30:24,511 | ^~~~~~~ 2024-04-03T12:31:17,832 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/definitions.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/definitions.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:31:17,997 building 'dinopy.fasta_reader' extension 2024-04-03T12:31:17,998 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/fasta_reader.c -o build/temp.linux-armv7l-cpython-311/dinopy/fasta_reader.o -O3 2024-04-03T12:31:18,622 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:31:18,622 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:31:18,623 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:31:18,624 from dinopy/fasta_reader.c:1271: 2024-04-03T12:31:18,624 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:31:18,625 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:31:18,626 | ^~~~~~~ 2024-04-03T12:31:57,967 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/fasta_reader.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/fasta_reader.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:31:58,179 building 'dinopy.fasta_writer' extension 2024-04-03T12:31:58,181 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/fasta_writer.c -o build/temp.linux-armv7l-cpython-311/dinopy/fasta_writer.o -O3 2024-04-03T12:31:58,683 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:31:58,684 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:31:58,685 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:31:58,685 from dinopy/fasta_writer.c:1271: 2024-04-03T12:31:58,686 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:31:58,686 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:31:58,687 | ^~~~~~~ 2024-04-03T12:32:24,744 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/fasta_writer.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/fasta_writer.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:32:24,889 building 'dinopy.fastq_reader' extension 2024-04-03T12:32:24,890 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/fastq_reader.c -o build/temp.linux-armv7l-cpython-311/dinopy/fastq_reader.o -O3 2024-04-03T12:32:25,285 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:32:25,286 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:32:25,287 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:32:25,287 from dinopy/fastq_reader.c:1269: 2024-04-03T12:32:25,288 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:32:25,288 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:32:25,289 | ^~~~~~~ 2024-04-03T12:32:47,128 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/fastq_reader.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/fastq_reader.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:32:47,313 building 'dinopy.fastq_writer' extension 2024-04-03T12:32:47,314 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/fastq_writer.c -o build/temp.linux-armv7l-cpython-311/dinopy/fastq_writer.o -O3 2024-04-03T12:32:47,743 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:32:47,744 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:32:47,745 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:32:47,745 from dinopy/fastq_writer.c:1271: 2024-04-03T12:32:47,746 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:32:47,747 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:32:47,748 | ^~~~~~~ 2024-04-03T12:33:04,868 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/fastq_writer.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/fastq_writer.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:33:05,037 building 'dinopy.input_opener' extension 2024-04-03T12:33:05,038 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/input_opener.c -o build/temp.linux-armv7l-cpython-311/dinopy/input_opener.o -O3 2024-04-03T12:33:16,753 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/input_opener.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/input_opener.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:33:16,915 building 'dinopy.processors' extension 2024-04-03T12:33:16,915 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/processors.c -o build/temp.linux-armv7l-cpython-311/dinopy/processors.o -O3 2024-04-03T12:33:17,314 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:33:17,314 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:33:17,315 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:33:17,316 from dinopy/processors.c:1271: 2024-04-03T12:33:17,316 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:33:17,317 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:33:17,317 | ^~~~~~~ 2024-04-03T12:34:33,103 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/processors.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/processors.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:34:33,360 building 'dinopy.shape' extension 2024-04-03T12:34:33,361 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/shape.c -o build/temp.linux-armv7l-cpython-311/dinopy/shape.o -O3 2024-04-03T12:34:33,798 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:34:33,799 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:34:33,800 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:34:33,800 from dinopy/shape.c:1269: 2024-04-03T12:34:33,801 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:34:33,802 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:34:33,802 | ^~~~~~~ 2024-04-03T12:34:49,181 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/shape.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/shape.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:34:49,311 building 'dinopy.shaping' extension 2024-04-03T12:34:49,312 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/shaping.c -o build/temp.linux-armv7l-cpython-311/dinopy/shaping.o -O3 2024-04-03T12:34:49,717 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:34:49,717 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:34:49,718 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:34:49,718 from dinopy/shaping.c:1269: 2024-04-03T12:34:49,719 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:34:49,719 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:34:49,720 | ^~~~~~~ 2024-04-03T12:34:50,109 dinopy/shaping.c: In function ‘__pyx_f_6dinopy_7shaping__apply_shape_int’: 2024-04-03T12:34:50,129 dinopy/shaping.c:22556:33: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 2024-04-03T12:34:50,129 22556 | for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_6; __pyx_t_1+=1) { 2024-04-03T12:34:50,130 | ^ 2024-04-03T12:35:27,296 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/shaping.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/shaping.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:35:27,460 building 'dinopy.output_opener' extension 2024-04-03T12:35:27,461 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/output_opener.c -o build/temp.linux-armv7l-cpython-311/dinopy/output_opener.o -O3 2024-04-03T12:35:45,388 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/output_opener.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/output_opener.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:35:45,520 building 'dinopy.nameline_parser' extension 2024-04-03T12:35:45,520 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/nameline_parser.c -o build/temp.linux-armv7l-cpython-311/dinopy/nameline_parser.o -O3 2024-04-03T12:36:09,423 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/nameline_parser.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/nameline_parser.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:36:09,572 building 'dinopy.sam_reader' extension 2024-04-03T12:36:09,573 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/sam_reader.c -o build/temp.linux-armv7l-cpython-311/dinopy/sam_reader.o -O3 2024-04-03T12:36:09,978 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:36:09,979 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:36:09,979 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:36:09,980 from dinopy/sam_reader.c:1271: 2024-04-03T12:36:09,980 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:36:09,981 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:36:09,981 | ^~~~~~~ 2024-04-03T12:36:29,453 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/sam_reader.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/sam_reader.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:36:29,807 building 'dinopy.sam_writer' extension 2024-04-03T12:36:29,808 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/sam_writer.c -o build/temp.linux-armv7l-cpython-311/dinopy/sam_writer.o -O3 2024-04-03T12:36:45,464 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/sam_writer.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/sam_writer.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:36:45,598 building 'dinopy.sambam' extension 2024-04-03T12:36:45,598 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include -I/usr/include/python3.11 -c dinopy/sambam.c -o build/temp.linux-armv7l-cpython-311/dinopy/sambam.o -O3 2024-04-03T12:36:46,012 In file included from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-04-03T12:36:46,012 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-04-03T12:36:46,013 from /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-04-03T12:36:46,014 from dinopy/sambam.c:1271: 2024-04-03T12:36:46,015 /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2024-04-03T12:36:46,015 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-04-03T12:36:46,016 | ^~~~~~~ 2024-04-03T12:37:16,295 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/sambam.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/sambam.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:37:16,446 building 'dinopy.wrap_sais' extension 2024-04-03T12:37:16,448 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idinopy -Idinopy/cpp/ -I/usr/include/python3.11 -c dinopy/wrap_sais.cpp -o build/temp.linux-armv7l-cpython-311/dinopy/wrap_sais.o -O3 2024-04-03T12:37:17,938 In file included from dinopy/wrap_sais.cpp:1257: 2024-04-03T12:37:17,939 dinopy/cpp/sais.cpp: In function ‘void SA_IS(unsigned char*, int*, int, int, int, int)’: 2024-04-03T12:37:17,939 dinopy/cpp/sais.cpp:10:83: warning: ‘*t_411 + _11’ is used uninitialized [-Wuninitialized] 2024-04-03T12:37:17,940 10 | #define tset(i, b) t[(i)/8]=(b) ? (mask[(i)%8]|t[(i)/8]) : ((~mask[(i)%8])&t[(i)/8]) 2024-04-03T12:37:17,940 | ^ 2024-04-03T12:37:19,512 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dinopy/wrap_sais.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dinopy/wrap_sais.cpython-311-arm-linux-gnueabihf.so 2024-04-03T12:37:19,678 installing to build/bdist.linux-armv7l/wheel 2024-04-03T12:37:19,679 running install 2024-04-03T12:37:19,702 running install_lib 2024-04-03T12:37:19,712 creating build/bdist.linux-armv7l 2024-04-03T12:37:19,712 creating build/bdist.linux-armv7l/wheel 2024-04-03T12:37:19,714 copying build/lib.linux-armv7l-cpython-311/README.rst -> build/bdist.linux-armv7l/wheel 2024-04-03T12:37:19,718 creating build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,719 copying build/lib.linux-armv7l-cpython-311/dinopy/exceptions.py -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,721 copying build/lib.linux-armv7l-cpython-311/dinopy/shaping.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,725 copying build/lib.linux-armv7l-cpython-311/dinopy/fasta_reader.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,728 copying build/lib.linux-armv7l-cpython-311/dinopy/__init__.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,730 copying build/lib.linux-armv7l-cpython-311/dinopy/sambam.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,733 copying build/lib.linux-armv7l-cpython-311/dinopy/output_opener.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,736 copying build/lib.linux-armv7l-cpython-311/dinopy/nameline_parser.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,764 copying build/lib.linux-armv7l-cpython-311/dinopy/auxiliary.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,775 copying build/lib.linux-armv7l-cpython-311/dinopy/sam_reader.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,777 copying build/lib.linux-armv7l-cpython-311/dinopy/sam_writer.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,779 copying build/lib.linux-armv7l-cpython-311/dinopy/definitions.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,781 copying build/lib.linux-armv7l-cpython-311/dinopy/shape.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,784 copying build/lib.linux-armv7l-cpython-311/dinopy/auxiliary.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,786 copying build/lib.linux-armv7l-cpython-311/dinopy/conversion.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,807 copying build/lib.linux-armv7l-cpython-311/dinopy/auxiliary.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,810 copying build/lib.linux-armv7l-cpython-311/dinopy/shaping.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,851 copying build/lib.linux-armv7l-cpython-311/dinopy/sam_reader.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,854 creating build/bdist.linux-armv7l/wheel/dinopy/cpp 2024-04-03T12:37:19,855 copying build/lib.linux-armv7l-cpython-311/dinopy/cpp/sais.cpp -> build/bdist.linux-armv7l/wheel/dinopy/cpp 2024-04-03T12:37:19,857 copying build/lib.linux-armv7l-cpython-311/dinopy/fastq_reader.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,859 copying build/lib.linux-armv7l-cpython-311/dinopy/input_opener.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,914 copying build/lib.linux-armv7l-cpython-311/dinopy/processors.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,916 copying build/lib.linux-armv7l-cpython-311/dinopy/__init__.py -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,917 copying build/lib.linux-armv7l-cpython-311/dinopy/fastq_writer.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,920 copying build/lib.linux-armv7l-cpython-311/dinopy/fastq_writer.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,933 copying build/lib.linux-armv7l-cpython-311/dinopy/fasta_writer.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,962 copying build/lib.linux-armv7l-cpython-311/dinopy/sambam.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,965 copying build/lib.linux-armv7l-cpython-311/dinopy/wrap_sais.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,967 copying build/lib.linux-armv7l-cpython-311/dinopy/nameline_parser.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:19,970 copying build/lib.linux-armv7l-cpython-311/dinopy/sam_writer.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,056 copying build/lib.linux-armv7l-cpython-311/dinopy/wrap_sais.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,063 copying build/lib.linux-armv7l-cpython-311/dinopy/fastq_reader.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,067 copying build/lib.linux-armv7l-cpython-311/dinopy/conversion.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,070 copying build/lib.linux-armv7l-cpython-311/dinopy/shape.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,095 copying build/lib.linux-armv7l-cpython-311/dinopy/sam_reader.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,119 copying build/lib.linux-armv7l-cpython-311/dinopy/sam_writer.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,122 copying build/lib.linux-armv7l-cpython-311/dinopy/creader.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,125 copying build/lib.linux-armv7l-cpython-311/dinopy/output_opener.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,150 copying build/lib.linux-armv7l-cpython-311/dinopy/creader.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,176 copying build/lib.linux-armv7l-cpython-311/dinopy/definitions.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,180 copying build/lib.linux-armv7l-cpython-311/dinopy/sambam.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,220 copying build/lib.linux-armv7l-cpython-311/dinopy/definitions.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,264 copying build/lib.linux-armv7l-cpython-311/dinopy/conversion.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,267 copying build/lib.linux-armv7l-cpython-311/dinopy/fastq_reader.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,292 copying build/lib.linux-armv7l-cpython-311/dinopy/creader.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,295 copying build/lib.linux-armv7l-cpython-311/dinopy/shaping.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,297 copying build/lib.linux-armv7l-cpython-311/dinopy/fasta_writer.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,301 copying build/lib.linux-armv7l-cpython-311/dinopy/output_opener.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,303 copying build/lib.linux-armv7l-cpython-311/dinopy/fasta_reader.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,375 copying build/lib.linux-armv7l-cpython-311/dinopy/wrap_sais.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,378 copying build/lib.linux-armv7l-cpython-311/dinopy/shape.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,380 copying build/lib.linux-armv7l-cpython-311/dinopy/fasta_reader.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,383 copying build/lib.linux-armv7l-cpython-311/dinopy/input_opener.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,386 copying build/lib.linux-armv7l-cpython-311/dinopy/fai_io.py -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,389 copying build/lib.linux-armv7l-cpython-311/dinopy/nameline_parser.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,391 copying build/lib.linux-armv7l-cpython-311/dinopy/fastq_writer.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,393 copying build/lib.linux-armv7l-cpython-311/dinopy/fasta_writer.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,395 copying build/lib.linux-armv7l-cpython-311/dinopy/input_opener.pxd -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,396 copying build/lib.linux-armv7l-cpython-311/dinopy/processors.pyx -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,401 copying build/lib.linux-armv7l-cpython-311/dinopy/processors.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/dinopy 2024-04-03T12:37:20,474 running install_egg_info 2024-04-03T12:37:20,491 running egg_info 2024-04-03T12:37:20,497 writing dinopy.egg-info/PKG-INFO 2024-04-03T12:37:20,500 writing dependency_links to dinopy.egg-info/dependency_links.txt 2024-04-03T12:37:20,502 writing requirements to dinopy.egg-info/requires.txt 2024-04-03T12:37:20,503 writing top-level names to dinopy.egg-info/top_level.txt 2024-04-03T12:37:20,517 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,518 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,519 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,519 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,520 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,520 dependency 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be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,544 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,545 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,545 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,546 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,547 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,547 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,548 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,548 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,549 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,550 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,550 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,551 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,551 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,552 dependency /tmp/pip-build-env-_p7s8k1e/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2024-04-03T12:37:20,559 ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any 2024-04-03T12:37:20,562 reading manifest file 'dinopy.egg-info/SOURCES.txt' 2024-04-03T12:37:20,579 reading manifest template 'MANIFEST.in' 2024-04-03T12:37:20,580 adding license file 'LICENSE.rst' 2024-04-03T12:37:20,581 adding license file 'AUTHORS.rst' 2024-04-03T12:37:20,586 writing manifest file 'dinopy.egg-info/SOURCES.txt' 2024-04-03T12:37:20,588 Copying dinopy.egg-info to build/bdist.linux-armv7l/wheel/dinopy-3.0.0-py3.11.egg-info 2024-04-03T12:37:20,599 running install_scripts 2024-04-03T12:37:20,647 creating build/bdist.linux-armv7l/wheel/dinopy-3.0.0.dist-info/WHEEL 2024-04-03T12:37:20,650 creating '/tmp/pip-wheel-rn0r_01_/.tmp-lkmwm7b8/dinopy-3.0.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-04-03T12:37:20,652 adding 'README.rst' 2024-04-03T12:37:20,655 adding 'dinopy/__init__.pxd' 2024-04-03T12:37:20,656 adding 'dinopy/__init__.py' 2024-04-03T12:37:20,757 adding 'dinopy/auxiliary.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:20,761 adding 'dinopy/auxiliary.pxd' 2024-04-03T12:37:20,762 adding 'dinopy/auxiliary.pyx' 2024-04-03T12:37:20,956 adding 'dinopy/conversion.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:20,964 adding 'dinopy/conversion.pxd' 2024-04-03T12:37:20,967 adding 'dinopy/conversion.pyx' 2024-04-03T12:37:21,113 adding 'dinopy/creader.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:21,119 adding 'dinopy/creader.pxd' 2024-04-03T12:37:21,120 adding 'dinopy/creader.pyx' 2024-04-03T12:37:21,380 adding 'dinopy/definitions.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:21,390 adding 'dinopy/definitions.pxd' 2024-04-03T12:37:21,393 adding 'dinopy/definitions.pyx' 2024-04-03T12:37:21,395 adding 'dinopy/exceptions.py' 2024-04-03T12:37:21,396 adding 'dinopy/fai_io.py' 2024-04-03T12:37:21,712 adding 'dinopy/fasta_reader.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:21,723 adding 'dinopy/fasta_reader.pxd' 2024-04-03T12:37:21,726 adding 'dinopy/fasta_reader.pyx' 2024-04-03T12:37:21,923 adding 'dinopy/fasta_writer.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:21,930 adding 'dinopy/fasta_writer.pxd' 2024-04-03T12:37:21,933 adding 'dinopy/fasta_writer.pyx' 2024-04-03T12:37:22,123 adding 'dinopy/fastq_reader.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:22,129 adding 'dinopy/fastq_reader.pxd' 2024-04-03T12:37:22,132 adding 'dinopy/fastq_reader.pyx' 2024-04-03T12:37:22,273 adding 'dinopy/fastq_writer.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:22,279 adding 'dinopy/fastq_writer.pxd' 2024-04-03T12:37:22,281 adding 'dinopy/fastq_writer.pyx' 2024-04-03T12:37:22,382 adding 'dinopy/input_opener.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:22,386 adding 'dinopy/input_opener.pxd' 2024-04-03T12:37:22,388 adding 'dinopy/input_opener.pyx' 2024-04-03T12:37:22,582 adding 'dinopy/nameline_parser.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:22,589 adding 'dinopy/nameline_parser.pxd' 2024-04-03T12:37:22,592 adding 'dinopy/nameline_parser.pyx' 2024-04-03T12:37:22,736 adding 'dinopy/output_opener.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:22,741 adding 'dinopy/output_opener.pxd' 2024-04-03T12:37:22,743 adding 'dinopy/output_opener.pyx' 2024-04-03T12:37:23,240 adding 'dinopy/processors.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:23,256 adding 'dinopy/processors.pxd' 2024-04-03T12:37:23,260 adding 'dinopy/processors.pyx' 2024-04-03T12:37:23,432 adding 'dinopy/sam_reader.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:23,438 adding 'dinopy/sam_reader.pxd' 2024-04-03T12:37:23,440 adding 'dinopy/sam_reader.pyx' 2024-04-03T12:37:23,577 adding 'dinopy/sam_writer.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:23,582 adding 'dinopy/sam_writer.pxd' 2024-04-03T12:37:23,583 adding 'dinopy/sam_writer.pyx' 2024-04-03T12:37:23,800 adding 'dinopy/sambam.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:23,808 adding 'dinopy/sambam.pxd' 2024-04-03T12:37:23,811 adding 'dinopy/sambam.pyx' 2024-04-03T12:37:23,950 adding 'dinopy/shape.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:23,955 adding 'dinopy/shape.pxd' 2024-04-03T12:37:23,957 adding 'dinopy/shape.pyx' 2024-04-03T12:37:24,265 adding 'dinopy/shaping.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:24,275 adding 'dinopy/shaping.pxd' 2024-04-03T12:37:24,277 adding 'dinopy/shaping.pyx' 2024-04-03T12:37:24,295 adding 'dinopy/wrap_sais.cpython-311-arm-linux-gnueabihf.so' 2024-04-03T12:37:24,296 adding 'dinopy/wrap_sais.pxd' 2024-04-03T12:37:24,298 adding 'dinopy/wrap_sais.pyx' 2024-04-03T12:37:24,300 adding 'dinopy/cpp/sais.cpp' 2024-04-03T12:37:24,302 adding 'dinopy-3.0.0.dist-info/AUTHORS.rst' 2024-04-03T12:37:24,303 adding 'dinopy-3.0.0.dist-info/LICENSE.rst' 2024-04-03T12:37:24,304 adding 'dinopy-3.0.0.dist-info/METADATA' 2024-04-03T12:37:24,306 adding 'dinopy-3.0.0.dist-info/WHEEL' 2024-04-03T12:37:24,307 adding 'dinopy-3.0.0.dist-info/top_level.txt' 2024-04-03T12:37:24,308 adding 'dinopy-3.0.0.dist-info/RECORD' 2024-04-03T12:37:24,428 removing build/bdist.linux-armv7l/wheel 2024-04-03T12:37:24,636 Building wheel for dinopy (pyproject.toml): finished with status 'done' 2024-04-03T12:37:24,763 Created wheel for dinopy: filename=dinopy-3.0.0-cp311-cp311-linux_armv7l.whl size=6905818 sha256=3155541d36a516547277e580862ec126d9c0ecc706ff522596f3381480c3c6c9 2024-04-03T12:37:24,764 Stored in directory: /tmp/pip-ephem-wheel-cache-by8t75lb/wheels/f1/cd/1c/ec02df2b7314b1ec4cd2970fc99fb00bbfede3a20fd949a136 2024-04-03T12:37:24,779 Successfully built dinopy 2024-04-03T12:37:25,026 Removed build tracker: '/tmp/pip-build-tracker-ulyt9xm7'