2022-12-17T17:54:45,083 Created temporary directory: /tmp/pip-ephem-wheel-cache-95dtqzb_ 2022-12-17T17:54:45,085 Created temporary directory: /tmp/pip-build-tracker-gkvo650r 2022-12-17T17:54:45,086 Initialized build tracking at /tmp/pip-build-tracker-gkvo650r 2022-12-17T17:54:45,086 Created build tracker: /tmp/pip-build-tracker-gkvo650r 2022-12-17T17:54:45,086 Entered build tracker: /tmp/pip-build-tracker-gkvo650r 2022-12-17T17:54:45,087 Created temporary directory: /tmp/pip-wheel-70_9h_r1 2022-12-17T17:54:45,090 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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https://files.pythonhosted.org/packages/e7/14/7d169a6807b2a80430e56df3d8a365fd77472666eca2699a406229e31a30/MDAnalysis-2.4.0-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,214 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/96/9d/08c32ba004d58c9c9b9113cb5026ec4f4787b5cbe909b35ac7fedde50582/MDAnalysis-2.4.0-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,215 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/98/8d/27b01addb197cd266414763403e88bbaaf2c4f3afa457a5d0f223d2cabbc/MDAnalysis-2.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,215 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/ac/19/a4a8d5000be7bcadf20b6150731d2aab5e0842e6313c7b2c7b4d121e7ca6/MDAnalysis-2.4.0-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,215 Found link https://files.pythonhosted.org/packages/a9/b0/67c19de6f80f4d0b2b465b3d5f94d347ce0d200d7da6ed7d9d91b712db4d/MDAnalysis-2.4.0.tar.gz (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8), version: 2.4.0 2022-12-17T17:54:45,216 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/27/59/cd13f05e4a4dba1a96f818ab99619cf45dd4980086a69326ef9d973073cd/MDAnalysis-2.4.1-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,216 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/9b/91/59b0303d555fe946144daeeb3484f8dae716ae78c4105d40647d83bda678/MDAnalysis-2.4.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,216 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/ba/9d/5f2429ee496079a2969b9b03850ab5fd5f5be242119b088855fd49f6f6e6/MDAnalysis-2.4.1-cp310-cp310-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,216 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/9d/ae/3ae3b51a0adb99099572052b05e6202efc2f1a02795ed8f9de5b2b0ef154/MDAnalysis-2.4.1-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,216 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/db/6e/b396db627091d47b6f224f02cb08739c8a8ef697ee9949f3d4be81cc8ddf/MDAnalysis-2.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,217 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/01/1e/a7dcf4f55b7dd624edaa4fa6b47d202fd3884c5b73ce13ac81fdaee0339b/MDAnalysis-2.4.1-cp311-cp311-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,217 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/c8/e5/1f68f743a1ad1b9a09d2047cc55c6565e5c835c2a444686e8458f5dac831/MDAnalysis-2.4.1-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,217 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/8a/3d/34bc8f592d832ec464e427ecf09c62898a128a41c3f1ae142a1d9f9f2646/MDAnalysis-2.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,217 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/a4/3f/c3961c791f4ab6128fbde66d5829b53d8e89a67ac3d4c23850b58c267206/MDAnalysis-2.4.1-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,217 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/3d/59/1a669cb57701c883c0b2e36742fd5d7a250a71fc24e369c57db71496481f/MDAnalysis-2.4.1-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,218 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/64/3f/4a0d22c2b5bad72be6c07c31c6e9e870e6b3a50142edc97962830bbe22ad/MDAnalysis-2.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,218 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/83/d8/e99fcc0339181b0ffe3fac620f884241bd502bb392696e2429984c3ea81d/MDAnalysis-2.4.1-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,218 Found link https://files.pythonhosted.org/packages/8f/c0/eba86324ca52fe66db629a4d805729ad8ac3364e3adad532c063b52b7051/MDAnalysis-2.4.1.tar.gz (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8), version: 2.4.1 2022-12-17T17:54:45,219 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdanalysis/ 2022-12-17T17:54:45,219 Getting page https://www.piwheels.org/simple/mdanalysis/ 2022-12-17T17:54:45,220 Found index url https://www.piwheels.org/simple 2022-12-17T17:54:45,413 Fetched page https://www.piwheels.org/simple/mdanalysis/ as text/html 2022-12-17T17:54:45,442 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.4.0-cp39-cp39-linux_armv7l.whl#sha256=89a99e9094d9455640680119bc09e7ea680423ed644c57a199c1f2c083589a01 (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,442 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.4.0-cp39-cp39-linux_armv6l.whl#sha256=89a99e9094d9455640680119bc09e7ea680423ed644c57a199c1f2c083589a01 (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-12-17T17:54:45,442 Skipping link: No binaries permitted for mdanalysis: 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(requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2022-12-17T17:54:45,447 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=1214ca3490e50243b48350c6c6a2c89b77cce8f1cd72f6d2549860b3db1ad84c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2022-12-17T17:54:45,447 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=e43dbbd4ecd06fb475d80e5dae571708415e1287e6dd2c669c98095e13ea2ae8 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,447 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp39-cp39-linux_armv6l.whl#sha256=e43dbbd4ecd06fb475d80e5dae571708415e1287e6dd2c669c98095e13ea2ae8 (from https://www.piwheels.org/simple/mdanalysis/) 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp34-cp34m-linux_armv6l.whl#sha256=34198e0f9e509df1779c2255812cee0f720dc8e989c7d4b7196337f75f1ef51b (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,458 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp34-cp34m-linux_armv7l.whl#sha256=34198e0f9e509df1779c2255812cee0f720dc8e989c7d4b7196337f75f1ef51b (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,458 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp35-cp35m-linux_armv7l.whl#sha256=032867bf17eecd5fd249607198ad5c191fac901f2856d5a485ffc53a8eb687d4 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,459 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp34-cp34m-linux_armv6l.whl#sha256=30c2bb9cf26e969dbdc8978bd4710e9e8a42ee42ed7c9ad506c63a0855448307 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,459 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp34-cp34m-linux_armv7l.whl#sha256=30c2bb9cf26e969dbdc8978bd4710e9e8a42ee42ed7c9ad506c63a0855448307 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,459 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp34-cp34m-linux_armv6l.whl#sha256=527918d821e76043cda119ee29aa26b835f8f85251d560d47616e9147b5a1539 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,460 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp34-cp34m-linux_armv7l.whl#sha256=527918d821e76043cda119ee29aa26b835f8f85251d560d47616e9147b5a1539 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,460 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp35-cp35m-linux_armv6l.whl#sha256=b9d6e5734efb33b9383183904d491de8ef28aeeac7bbfdd617d48084126af113 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,460 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp35-cp35m-linux_armv7l.whl#sha256=b9d6e5734efb33b9383183904d491de8ef28aeeac7bbfdd617d48084126af113 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,460 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp39-cp39-linux_armv7l.whl#sha256=ef25ee9269f3b7f8ab95f1c3c563c39740fd2b7801df49d6be7e702c7db7f8fc (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,460 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp39-cp39-linux_armv6l.whl#sha256=ef25ee9269f3b7f8ab95f1c3c563c39740fd2b7801df49d6be7e702c7db7f8fc (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,461 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp35-cp35m-linux_armv7l.whl#sha256=46ca86446af4c56b5805a1cb36dd77ac64d009abb5500878ea4fa26320c7ba43 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,461 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp35-cp35m-linux_armv6l.whl#sha256=46ca86446af4c56b5805a1cb36dd77ac64d009abb5500878ea4fa26320c7ba43 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,461 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp34-cp34m-linux_armv6l.whl#sha256=89151b95fc0cd948f7a2d1d660b8c2453a612a752a2a2d7d8fb6d169ff2782d4 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,461 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp34-cp34m-linux_armv7l.whl#sha256=89151b95fc0cd948f7a2d1d660b8c2453a612a752a2a2d7d8fb6d169ff2782d4 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,461 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp37-cp37m-linux_armv7l.whl#sha256=a073eda71f157be82bd9b81ac12793e63834dde1ac9b63ca704668a88b025c1e (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,462 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp37-cp37m-linux_armv6l.whl#sha256=a073eda71f157be82bd9b81ac12793e63834dde1ac9b63ca704668a88b025c1e (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,462 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp35-cp35m-linux_armv7l.whl#sha256=47de147e5ee68a99b75107632aaa1e3bf84b4fa1f5bd7a456c1537266d437fbb (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,462 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp35-cp35m-linux_armv6l.whl#sha256=47de147e5ee68a99b75107632aaa1e3bf84b4fa1f5bd7a456c1537266d437fbb (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,462 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp34-cp34m-linux_armv6l.whl#sha256=a0ddeb70a574aee9a5c491f2da635dc26e5e5b2b4cac7d8abbbffb3c1b4c7a8a (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,462 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp34-cp34m-linux_armv7l.whl#sha256=a0ddeb70a574aee9a5c491f2da635dc26e5e5b2b4cac7d8abbbffb3c1b4c7a8a (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,463 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp35-cp35m-linux_armv6l.whl#sha256=28a9bbed8fd84f6ebdf4efb48ef9e2435715169ef7a558ad7f11a33232e83815 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,463 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp35-cp35m-linux_armv7l.whl#sha256=28a9bbed8fd84f6ebdf4efb48ef9e2435715169ef7a558ad7f11a33232e83815 (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,463 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp34-cp34m-linux_armv6l.whl#sha256=6d813f8dee5bde52fe344b851079bfaab34030f253869d7098ee33929566e36a (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,463 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp34-cp34m-linux_armv7l.whl#sha256=6d813f8dee5bde52fe344b851079bfaab34030f253869d7098ee33929566e36a (from https://www.piwheels.org/simple/mdanalysis/) 2022-12-17T17:54:45,464 Skipping link: not a file: https://www.piwheels.org/simple/mdanalysis/ 2022-12-17T17:54:45,464 Skipping link: not a file: https://pypi.org/simple/mdanalysis/ 2022-12-17T17:54:45,486 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates 2022-12-17T17:54:45,503 Collecting mdanalysis==2.4.1 2022-12-17T17:54:45,505 Created temporary directory: /tmp/pip-unpack-9eb_lc2b 2022-12-17T17:54:45,731 Downloading MDAnalysis-2.4.1.tar.gz (3.7 MB) 2022-12-17T17:54:48,979 Added mdanalysis==2.4.1 from https://files.pythonhosted.org/packages/8f/c0/eba86324ca52fe66db629a4d805729ad8ac3364e3adad532c063b52b7051/MDAnalysis-2.4.1.tar.gz to build tracker '/tmp/pip-build-tracker-gkvo650r' 2022-12-17T17:54:49,032 Created temporary directory: /tmp/pip-build-env-m68reu_b 2022-12-17T17:54:49,040 Installing build dependencies: started 2022-12-17T17:54:49,041 Running command pip subprocess to install build dependencies 2022-12-17T17:54:50,295 Using pip 22.3 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2022-12-17T17:54:50,702 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2022-12-17T17:54:50,728 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-12-17T17:54:50,729 Ignoring numpy: markers 'python_version == "3.8" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_python_implementation != "PyPy"' don't match your environment 2022-12-17T17:54:50,731 Ignoring numpy: markers 'python_version == "3.8" and platform_machine == "arm64" and platform_system == "Darwin" and platform_python_implementation != "PyPy"' don't match your environment 2022-12-17T17:54:50,732 Ignoring numpy: markers 'python_version == "3.9" and platform_machine == "arm64" and platform_system == "Darwin" and platform_python_implementation != "PyPy"' don't match your environment 2022-12-17T17:54:50,733 Ignoring numpy: markers 'python_version == "3.10" and platform_system == "Windows" and platform_python_implementation != "PyPy"' don't match your environment 2022-12-17T17:54:50,734 Ignoring numpy: markers 'python_version == "3.10" and platform_system != "Windows" and platform_python_implementation != "PyPy"' don't match your environment 2022-12-17T17:54:50,735 Ignoring numpy: markers 'python_version == "3.11" and platform_python_implementation != "PyPy"' don't match your environment 2022-12-17T17:54:50,736 Ignoring numpy: markers 'python_version >= "3.12"' don't match your environment 2022-12-17T17:54:52,244 Collecting Cython>=0.28 2022-12-17T17:54:52,750 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.32-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-12-17T17:54:53,089 Collecting packaging 2022-12-17T17:54:53,108 Using cached https://www.piwheels.org/simple/packaging/packaging-22.0-py3-none-any.whl (42 kB) 2022-12-17T17:54:54,543 Collecting numpy==1.20.0 2022-12-17T17:54:55,683 Using cached https://www.piwheels.org/simple/numpy/numpy-1.20.0-cp39-cp39-linux_armv7l.whl (11.6 MB) 2022-12-17T17:54:57,461 Collecting setuptools 2022-12-17T17:54:57,612 Using cached https://www.piwheels.org/simple/setuptools/setuptools-65.6.3-py3-none-any.whl (1.2 MB) 2022-12-17T17:54:57,908 Collecting wheel 2022-12-17T17:54:57,925 Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB) 2022-12-17T17:54:59,794 Installing collected packages: wheel, setuptools, packaging, numpy, Cython 2022-12-17T17:54:59,954 Creating /tmp/pip-build-env-m68reu_b/overlay/bin 2022-12-17T17:54:59,957 changing mode of /tmp/pip-build-env-m68reu_b/overlay/bin/wheel to 755 2022-12-17T17:55:10,830 changing mode of /tmp/pip-build-env-m68reu_b/overlay/bin/f2py to 755 2022-12-17T17:55:10,833 changing mode of /tmp/pip-build-env-m68reu_b/overlay/bin/f2py3 to 755 2022-12-17T17:55:10,835 changing mode of /tmp/pip-build-env-m68reu_b/overlay/bin/f2py3.9 to 755 2022-12-17T17:55:13,740 changing mode of /tmp/pip-build-env-m68reu_b/overlay/bin/cygdb to 755 2022-12-17T17:55:13,742 changing mode of /tmp/pip-build-env-m68reu_b/overlay/bin/cython to 755 2022-12-17T17:55:13,744 changing mode of /tmp/pip-build-env-m68reu_b/overlay/bin/cythonize to 755 2022-12-17T17:55:13,771 Successfully installed Cython-0.29.32 numpy-1.20.0 packaging-22.0 setuptools-65.6.3 wheel-0.38.4 2022-12-17T17:55:13,785 [notice] A new release of pip available: 22.3 -> 22.3.1 2022-12-17T17:55:13,785 [notice] To update, run: python3 -m pip install --upgrade pip 2022-12-17T17:55:14,190 Installing build dependencies: finished with status 'done' 2022-12-17T17:55:14,204 Getting requirements to build wheel: started 2022-12-17T17:55:14,205 Running command Getting requirements to build wheel 2022-12-17T17:55:54,987 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-12-17T17:55:54,988 Will attempt to use Cython. 2022-12-17T17:55:54,988 Compiling MDAnalysis/lib/formats/libdcd.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,988 Compiling MDAnalysis/lib/c_distances.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,988 Compiling MDAnalysis/lib/c_distances_openmp.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,988 Compiling MDAnalysis/lib/qcprot.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,988 Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,989 Compiling MDAnalysis/lib/formats/cython_util.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,989 Compiling MDAnalysis/analysis/encore/cutils.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,989 Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,989 Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2022-12-17T17:55:54,989 Compiling MDAnalysis/lib/_cutil.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-12-17T17:55:54,990 Compiling MDAnalysis/lib/_augment.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-12-17T17:55:54,990 Compiling MDAnalysis/lib/nsgrid.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2022-12-17T17:55:54,990 Compiling MDAnalysis/coordinates/timestep.pyx because it depends on /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/__init__.pxd. 2022-12-17T17:55:54,990 [ 1/13] Cythonizing MDAnalysis/lib/_augment.pyx 2022-12-17T17:55:54,990 [ 2/13] Cythonizing MDAnalysis/lib/_cutil.pyx 2022-12-17T17:55:54,990 [ 3/13] Cythonizing MDAnalysis/lib/nsgrid.pyx 2022-12-17T17:55:54,990 [ 4/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx 2022-12-17T17:55:54,991 [ 5/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx 2022-12-17T17:55:54,991 [ 6/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx 2022-12-17T17:55:54,991 [ 7/13] Cythonizing MDAnalysis/coordinates/timestep.pyx 2022-12-17T17:55:54,991 [ 8/13] Cythonizing MDAnalysis/lib/c_distances.pyx 2022-12-17T17:55:54,991 [ 9/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx 2022-12-17T17:55:54,992 [10/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx 2022-12-17T17:55:54,992 [11/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx 2022-12-17T17:55:54,992 [12/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx 2022-12-17T17:55:54,992 [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx 2022-12-17T17:55:56,051 Getting requirements to build wheel: finished with status 'done' 2022-12-17T17:55:56,065 Created temporary directory: /tmp/pip-modern-metadata-706bvjta 2022-12-17T17:55:56,068 Preparing metadata (pyproject.toml): started 2022-12-17T17:55:56,069 Running command Preparing metadata (pyproject.toml) 2022-12-17T17:55:58,427 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-12-17T17:55:58,428 Will attempt to use Cython. 2022-12-17T17:55:58,637 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:196: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2022-12-17T17:55:58,637 warnings.warn(msg) 2022-12-17T17:55:58,848 running dist_info 2022-12-17T17:55:58,857 creating /tmp/pip-modern-metadata-706bvjta/MDAnalysis.egg-info 2022-12-17T17:55:58,863 writing /tmp/pip-modern-metadata-706bvjta/MDAnalysis.egg-info/PKG-INFO 2022-12-17T17:55:58,868 writing dependency_links to /tmp/pip-modern-metadata-706bvjta/MDAnalysis.egg-info/dependency_links.txt 2022-12-17T17:55:58,871 writing requirements to /tmp/pip-modern-metadata-706bvjta/MDAnalysis.egg-info/requires.txt 2022-12-17T17:55:58,873 writing top-level names to /tmp/pip-modern-metadata-706bvjta/MDAnalysis.egg-info/top_level.txt 2022-12-17T17:55:58,874 writing manifest file '/tmp/pip-modern-metadata-706bvjta/MDAnalysis.egg-info/SOURCES.txt' 2022-12-17T17:55:58,922 reading manifest file '/tmp/pip-modern-metadata-706bvjta/MDAnalysis.egg-info/SOURCES.txt' 2022-12-17T17:55:58,926 reading manifest template 'MANIFEST.in' 2022-12-17T17:55:59,113 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2022-12-17T17:55:59,114 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2022-12-17T17:55:59,116 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2022-12-17T17:55:59,117 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2022-12-17T17:55:59,119 warning: no previously-included files matching '*~' found anywhere in distribution 2022-12-17T17:55:59,120 warning: no previously-included files matching '.git' found anywhere in distribution 2022-12-17T17:55:59,120 adding license file 'LICENSE' 2022-12-17T17:55:59,120 adding license file 'AUTHORS' 2022-12-17T17:55:59,139 writing manifest file '/tmp/pip-modern-metadata-706bvjta/MDAnalysis.egg-info/SOURCES.txt' 2022-12-17T17:55:59,141 creating '/tmp/pip-modern-metadata-706bvjta/MDAnalysis-2.4.1.dist-info' 2022-12-17T17:55:59,449 Preparing metadata (pyproject.toml): finished with status 'done' 2022-12-17T17:55:59,460 Source in /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25 has version 2.4.1, which satisfies requirement mdanalysis==2.4.1 from https://files.pythonhosted.org/packages/8f/c0/eba86324ca52fe66db629a4d805729ad8ac3364e3adad532c063b52b7051/MDAnalysis-2.4.1.tar.gz 2022-12-17T17:55:59,461 Removed mdanalysis==2.4.1 from https://files.pythonhosted.org/packages/8f/c0/eba86324ca52fe66db629a4d805729ad8ac3364e3adad532c063b52b7051/MDAnalysis-2.4.1.tar.gz from build tracker '/tmp/pip-build-tracker-gkvo650r' 2022-12-17T17:55:59,471 Created temporary directory: /tmp/pip-unpack-6paqxvnl 2022-12-17T17:55:59,472 Building wheels for collected packages: mdanalysis 2022-12-17T17:55:59,476 Created temporary directory: /tmp/pip-wheel-voz9plh5 2022-12-17T17:55:59,477 Destination directory: /tmp/pip-wheel-voz9plh5 2022-12-17T17:55:59,479 Building wheel for mdanalysis (pyproject.toml): started 2022-12-17T17:55:59,480 Running command Building wheel for mdanalysis (pyproject.toml) 2022-12-17T17:56:01,756 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-12-17T17:56:01,757 Will attempt to use Cython. 2022-12-17T17:56:01,958 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:196: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2022-12-17T17:56:01,958 warnings.warn(msg) 2022-12-17T17:56:02,154 running bdist_wheel 2022-12-17T17:56:02,174 running build 2022-12-17T17:56:02,174 running build_py 2022-12-17T17:56:02,181 creating build 2022-12-17T17:56:02,181 creating build/lib.linux-armv7l-cpython-39 2022-12-17T17:56:02,182 creating build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-12-17T17:56:02,184 copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-12-17T17:56:02,186 copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-12-17T17:56:02,189 copying MDAnalysis/due.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-12-17T17:56:02,191 copying MDAnalysis/authors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-12-17T17:56:02,193 copying MDAnalysis/units.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-12-17T17:56:02,196 copying MDAnalysis/version.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-12-17T17:56:02,198 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-12-17T17:56:02,217 copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-12-17T17:56:02,221 copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-12-17T17:56:02,224 copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-12-17T17:56:02,227 copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-12-17T17:56:02,229 copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-12-17T17:56:02,233 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,234 copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,236 copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,241 copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,244 copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,248 copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,255 copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,258 copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,262 copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,265 copying MDAnalysis/core/accessors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-12-17T17:56:02,268 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2022-12-17T17:56:02,269 copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2022-12-17T17:56:02,271 copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2022-12-17T17:56:02,274 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,275 copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,278 copying MDAnalysis/transformations/wrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,281 copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,283 copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,286 copying MDAnalysis/transformations/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,288 copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,291 copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,293 copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-12-17T17:56:02,296 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,297 copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,300 copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,303 copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,307 copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,310 copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,313 copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,316 copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,319 copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,323 copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,327 copying MDAnalysis/lib/correlations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:02,331 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-12-17T17:56:02,332 copying MDAnalysis/converters/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-12-17T17:56:02,334 copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-12-17T17:56:02,337 copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-12-17T17:56:02,339 copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-12-17T17:56:02,342 copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-12-17T17:56:02,344 copying MDAnalysis/converters/RDKit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-12-17T17:56:02,348 copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-12-17T17:56:02,352 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,353 copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,355 copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,358 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,360 copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,363 copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,366 copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,369 copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,373 copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,375 copying MDAnalysis/analysis/bat.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,378 copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,382 copying MDAnalysis/analysis/msd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,385 copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,388 copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,391 copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,394 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,397 copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,401 copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,404 copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,406 copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,409 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,412 copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,414 copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,417 copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:56:02,421 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,422 copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,426 copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,429 copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,431 copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,435 copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,437 copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,440 copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,444 copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,447 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,449 copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,451 copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,454 copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,456 copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,459 copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,461 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,464 copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,467 copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,471 copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,473 copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,476 copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,479 copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,481 copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,485 copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,487 copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,489 copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,492 copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,495 copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,498 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,500 copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,502 copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,506 copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,508 copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,511 copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:02,514 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2022-12-17T17:56:02,515 copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2022-12-17T17:56:02,517 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2022-12-17T17:56:02,520 copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2022-12-17T17:56:02,525 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,543 copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,546 copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,549 copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,552 copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,555 copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,558 copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,561 copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,565 copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,567 copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,570 copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,573 copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,576 copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,579 copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,582 copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,585 copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,588 copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,591 copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,594 copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,596 copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,599 copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,601 copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,604 copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,607 copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,609 copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,612 copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,615 copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,617 copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,620 copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-12-17T17:56:02,624 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-12-17T17:56:02,625 copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-12-17T17:56:02,627 copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-12-17T17:56:02,630 copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-12-17T17:56:02,632 copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-12-17T17:56:02,635 copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-12-17T17:56:02,638 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-12-17T17:56:02,641 copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-12-17T17:56:02,644 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:02,645 copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:02,649 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2022-12-17T17:56:02,650 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2022-12-17T17:56:02,653 copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2022-12-17T17:56:02,655 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-12-17T17:56:02,657 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-12-17T17:56:02,660 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-12-17T17:56:02,663 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-12-17T17:56:02,667 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-12-17T17:56:02,670 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-12-17T17:56:02,672 copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-12-17T17:56:02,675 copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-12-17T17:56:02,680 copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-12-17T17:56:02,684 copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-12-17T17:56:02,688 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-12-17T17:56:02,689 copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-12-17T17:56:02,692 copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-12-17T17:56:02,695 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2022-12-17T17:56:02,696 copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2022-12-17T17:56:02,699 copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2022-12-17T17:56:02,703 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:02,705 copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:02,708 copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:02,711 copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:02,713 copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:02,716 copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:02,719 copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:02,724 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T17:56:02,726 copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T17:56:02,729 copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T17:56:02,732 copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T17:56:02,737 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-12-17T17:56:02,738 copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-12-17T17:56:02,741 copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-12-17T17:56:02,744 copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-12-17T17:56:02,747 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-12-17T17:56:02,751 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-12-17T17:56:02,752 copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-12-17T17:56:02,756 copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-12-17T17:56:02,759 copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-12-17T17:56:02,762 copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-12-17T17:56:02,765 running egg_info 2022-12-17T17:56:02,778 writing MDAnalysis.egg-info/PKG-INFO 2022-12-17T17:56:02,783 writing dependency_links to MDAnalysis.egg-info/dependency_links.txt 2022-12-17T17:56:02,786 writing requirements to MDAnalysis.egg-info/requires.txt 2022-12-17T17:56:02,788 writing top-level names to MDAnalysis.egg-info/top_level.txt 2022-12-17T17:56:02,819 reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2022-12-17T17:56:02,832 reading manifest template 'MANIFEST.in' 2022-12-17T17:56:03,040 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2022-12-17T17:56:03,043 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2022-12-17T17:56:03,046 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2022-12-17T17:56:03,049 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2022-12-17T17:56:03,052 warning: no previously-included files matching '*~' found anywhere in distribution 2022-12-17T17:56:03,054 warning: no previously-included files matching '.git' found anywhere in distribution 2022-12-17T17:56:03,055 adding license file 'LICENSE' 2022-12-17T17:56:03,055 adding license file 'AUTHORS' 2022-12-17T17:56:03,080 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2022-12-17T17:56:03,170 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.include' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,171 !! 2022-12-17T17:56:03,171 ############################ 2022-12-17T17:56:03,171 # Package would be ignored # 2022-12-17T17:56:03,171 ############################ 2022-12-17T17:56:03,171 Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package, 2022-12-17T17:56:03,171 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,172 'MDAnalysis.analysis.encore.clustering.include' has been automatically added to the distribution only 2022-12-17T17:56:03,172 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,172 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,172 Please make sure that 'MDAnalysis.analysis.encore.clustering.include' is included as a package by using 2022-12-17T17:56:03,172 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,172 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,172 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,173 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,173 documentation page. 2022-12-17T17:56:03,173 !! 2022-12-17T17:56:03,173 check.warn(importable) 2022-12-17T17:56:03,174 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.src' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,174 !! 2022-12-17T17:56:03,174 ############################ 2022-12-17T17:56:03,175 # Package would be ignored # 2022-12-17T17:56:03,175 ############################ 2022-12-17T17:56:03,175 Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package, 2022-12-17T17:56:03,175 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,175 'MDAnalysis.analysis.encore.clustering.src' has been automatically added to the distribution only 2022-12-17T17:56:03,175 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,175 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,176 Please make sure that 'MDAnalysis.analysis.encore.clustering.src' is included as a package by using 2022-12-17T17:56:03,176 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,176 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,176 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,176 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,176 documentation page. 2022-12-17T17:56:03,177 !! 2022-12-17T17:56:03,177 check.warn(importable) 2022-12-17T17:56:03,177 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,178 !! 2022-12-17T17:56:03,178 ############################ 2022-12-17T17:56:03,178 # Package would be ignored # 2022-12-17T17:56:03,178 ############################ 2022-12-17T17:56:03,178 Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package, 2022-12-17T17:56:03,178 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,179 'MDAnalysis.analysis.encore.dimensionality_reduction.include' has been automatically added to the distribution only 2022-12-17T17:56:03,179 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,179 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,179 Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is included as a package by using 2022-12-17T17:56:03,179 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,179 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,179 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,180 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,180 documentation page. 2022-12-17T17:56:03,180 !! 2022-12-17T17:56:03,180 check.warn(importable) 2022-12-17T17:56:03,191 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,191 !! 2022-12-17T17:56:03,191 ############################ 2022-12-17T17:56:03,191 # Package would be ignored # 2022-12-17T17:56:03,191 ############################ 2022-12-17T17:56:03,192 Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package, 2022-12-17T17:56:03,192 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,192 'MDAnalysis.analysis.encore.dimensionality_reduction.src' has been automatically added to the distribution only 2022-12-17T17:56:03,192 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,192 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,192 Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is included as a package by using 2022-12-17T17:56:03,192 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,193 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,193 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,193 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,193 documentation page. 2022-12-17T17:56:03,193 !! 2022-12-17T17:56:03,194 check.warn(importable) 2022-12-17T17:56:03,194 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.include' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,194 !! 2022-12-17T17:56:03,194 ############################ 2022-12-17T17:56:03,194 # Package would be ignored # 2022-12-17T17:56:03,194 ############################ 2022-12-17T17:56:03,194 Python recognizes 'MDAnalysis.lib.formats.include' as an importable package, 2022-12-17T17:56:03,195 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,195 'MDAnalysis.lib.formats.include' has been automatically added to the distribution only 2022-12-17T17:56:03,195 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,195 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,195 Please make sure that 'MDAnalysis.lib.formats.include' is included as a package by using 2022-12-17T17:56:03,195 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,195 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,196 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,196 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,196 documentation page. 2022-12-17T17:56:03,196 !! 2022-12-17T17:56:03,196 check.warn(importable) 2022-12-17T17:56:03,197 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.src' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,197 !! 2022-12-17T17:56:03,197 ############################ 2022-12-17T17:56:03,197 # Package would be ignored # 2022-12-17T17:56:03,197 ############################ 2022-12-17T17:56:03,197 Python recognizes 'MDAnalysis.lib.formats.src' as an importable package, 2022-12-17T17:56:03,197 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,198 'MDAnalysis.lib.formats.src' has been automatically added to the distribution only 2022-12-17T17:56:03,198 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,198 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,198 Please make sure that 'MDAnalysis.lib.formats.src' is included as a package by using 2022-12-17T17:56:03,198 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,198 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,199 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,199 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,199 documentation page. 2022-12-17T17:56:03,199 !! 2022-12-17T17:56:03,199 check.warn(importable) 2022-12-17T17:56:03,200 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.include' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,200 !! 2022-12-17T17:56:03,200 ############################ 2022-12-17T17:56:03,200 # Package would be ignored # 2022-12-17T17:56:03,200 ############################ 2022-12-17T17:56:03,200 Python recognizes 'MDAnalysis.lib.include' as an importable package, 2022-12-17T17:56:03,201 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,201 'MDAnalysis.lib.include' has been automatically added to the distribution only 2022-12-17T17:56:03,201 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,201 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,201 Please make sure that 'MDAnalysis.lib.include' is included as a package by using 2022-12-17T17:56:03,201 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,201 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,202 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,202 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,202 documentation page. 2022-12-17T17:56:03,202 !! 2022-12-17T17:56:03,202 check.warn(importable) 2022-12-17T17:56:03,203 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.libmdanalysis' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,203 !! 2022-12-17T17:56:03,203 ############################ 2022-12-17T17:56:03,203 # Package would be ignored # 2022-12-17T17:56:03,203 ############################ 2022-12-17T17:56:03,203 Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package, 2022-12-17T17:56:03,203 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,204 'MDAnalysis.lib.libmdanalysis' has been automatically added to the distribution only 2022-12-17T17:56:03,204 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,204 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,204 Please make sure that 'MDAnalysis.lib.libmdanalysis' is included as a package by using 2022-12-17T17:56:03,204 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,204 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,205 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,205 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,205 documentation page. 2022-12-17T17:56:03,205 !! 2022-12-17T17:56:03,206 check.warn(importable) 2022-12-17T17:56:03,206 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.src.transformations' as data is deprecated, please list it in `packages`. 2022-12-17T17:56:03,206 !! 2022-12-17T17:56:03,206 ############################ 2022-12-17T17:56:03,206 # Package would be ignored # 2022-12-17T17:56:03,207 ############################ 2022-12-17T17:56:03,207 Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package, 2022-12-17T17:56:03,207 but it is not listed in the `packages` configuration of setuptools. 2022-12-17T17:56:03,208 'MDAnalysis.lib.src.transformations' has been automatically added to the distribution only 2022-12-17T17:56:03,208 because it may contain data files, but this behavior is likely to change 2022-12-17T17:56:03,208 in future versions of setuptools (and therefore is considered deprecated). 2022-12-17T17:56:03,208 Please make sure that 'MDAnalysis.lib.src.transformations' is included as a package by using 2022-12-17T17:56:03,208 the `packages` configuration field or the proper discovery methods 2022-12-17T17:56:03,209 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2022-12-17T17:56:03,209 instead of `find_packages(...)`/`find:`). 2022-12-17T17:56:03,209 You can read more about "package discovery" and "data files" on setuptools 2022-12-17T17:56:03,209 documentation page. 2022-12-17T17:56:03,209 !! 2022-12-17T17:56:03,210 check.warn(importable) 2022-12-17T17:56:03,210 copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-12-17T17:56:03,210 copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-12-17T17:56:03,214 copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,244 copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,247 copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,285 copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,287 copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,290 copying MDAnalysis/lib/c_distances.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,321 copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,324 copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,334 copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,337 copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,364 copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,368 copying MDAnalysis/lib/qcprot.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,388 copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,391 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include 2022-12-17T17:56:03,392 copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include 2022-12-17T17:56:03,395 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis 2022-12-17T17:56:03,396 copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis 2022-12-17T17:56:03,399 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src 2022-12-17T17:56:03,399 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2022-12-17T17:56:03,400 copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2022-12-17T17:56:03,403 copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2022-12-17T17:56:03,405 copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2022-12-17T17:56:03,410 copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:03,431 copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:03,433 copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T17:56:03,436 copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,457 copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,459 copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,461 copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,491 copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,494 copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,497 copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,527 copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,530 copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,533 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,534 copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,537 copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,540 copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,543 copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,546 copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,549 copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,552 copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,554 copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2022-12-17T17:56:03,557 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2022-12-17T17:56:03,558 copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2022-12-17T17:56:03,561 copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2022-12-17T17:56:03,565 copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2022-12-17T17:56:03,568 copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2022-12-17T17:56:03,570 copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2022-12-17T17:56:03,573 copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:03,581 copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:56:03,583 copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T17:56:03,592 copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T17:56:03,594 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include 2022-12-17T17:56:03,595 copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include 2022-12-17T17:56:03,597 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2022-12-17T17:56:03,598 copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2022-12-17T17:56:03,600 copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-12-17T17:56:03,611 copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-12-17T17:56:03,613 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include 2022-12-17T17:56:03,614 copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include 2022-12-17T17:56:03,617 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2022-12-17T17:56:03,618 copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2022-12-17T17:56:03,637 running build_ext 2022-12-17T17:56:03,638 building 'MDAnalysis.lib.formats.libdcd' extension 2022-12-17T17:56:03,639 creating build/temp.linux-armv7l-cpython-39 2022-12-17T17:56:03,640 creating build/temp.linux-armv7l-cpython-39/MDAnalysis 2022-12-17T17:56:03,641 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib 2022-12-17T17:56:03,642 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-12-17T17:56:03,643 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/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:56:03,682 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:56:04,067 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:56:04,067 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:56:04,067 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:56:04,068 from MDAnalysis/lib/formats/libdcd.c:781: 2022-12-17T17:56:04,068 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:56:04,068 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:56:04,068 | ^~~~~~~ 2022-12-17T17:56:04,166 In file included from MDAnalysis/lib/formats/libdcd.c:791: 2022-12-17T17:56:04,166 MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’: 2022-12-17T17:56:04,167 MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-12-17T17:56:04,167 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2022-12-17T17:56:04,167 | ^~ 2022-12-17T17:56:04,170 MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’: 2022-12-17T17:56:04,171 MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable] 2022-12-17T17:56:04,171 698 | struct tm *tmbuf; 2022-12-17T17:56:04,171 | ^~~~~ 2022-12-17T17:56:04,172 MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable] 2022-12-17T17:56:04,172 697 | time_t cur_time; 2022-12-17T17:56:04,172 | ^~~~~~~~ 2022-12-17T17:56:05,904 In file included from MDAnalysis/lib/formats/include/readdcd.h:25, 2022-12-17T17:56:05,904 from MDAnalysis/lib/formats/libdcd.c:791: 2022-12-17T17:56:05,905 At top level: 2022-12-17T17:56:05,905 MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2022-12-17T17:56:05,906 96 | static void swap2_aligned(void *v, long ndata) { 2022-12-17T17:56:05,906 | ^~~~~~~~~~~~~ 2022-12-17T17:56:05,906 MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2022-12-17T17:56:05,906 32 | static void swap2_unaligned(void *v, long ndata) { 2022-12-17T17:56:05,906 | ^~~~~~~~~~~~~~~ 2022-12-17T17:56:05,906 In file included from MDAnalysis/lib/formats/libdcd.c:790: 2022-12-17T17:56:05,907 MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2022-12-17T17:56:05,907 453 | static int fio_write_str(fio_fd fd, const char *str) { 2022-12-17T17:56:05,907 | ^~~~~~~~~~~~~ 2022-12-17T17:56:05,907 MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2022-12-17T17:56:05,907 449 | static int fio_read_int32(fio_fd fd, int *i) { 2022-12-17T17:56:05,907 | ^~~~~~~~~~~~~~ 2022-12-17T17:56:36,797 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:56:37,013 building 'MDAnalysis.lib.c_distances' extension 2022-12-17T17:56:37,014 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:56:37,047 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:56:37,402 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:56:37,402 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:56:37,402 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:56:37,402 from MDAnalysis/lib/c_distances.c:781: 2022-12-17T17:56:37,402 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:56:37,403 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:56:37,403 | ^~~~~~~ 2022-12-17T17:57:12,686 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:57:12,977 building 'MDAnalysis.lib.c_distances_openmp' extension 2022-12-17T17:57:12,978 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 -DPARALLEL -I/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:57:13,009 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:57:13,321 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:57:13,321 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:57:13,322 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:57:13,322 from MDAnalysis/lib/c_distances_openmp.c:792: 2022-12-17T17:57:13,322 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:57:13,322 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:57:13,322 | ^~~~~~~ 2022-12-17T17:57:19,047 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib -lm -lgomp -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -fopenmp 2022-12-17T17:57:19,214 building 'MDAnalysis.lib.qcprot' extension 2022-12-17T17:57:19,215 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:57:19,251 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:57:19,583 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:57:19,583 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:57:19,583 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:57:19,583 from MDAnalysis/lib/qcprot.c:775: 2022-12-17T17:57:19,583 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:57:19,584 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:57:19,584 | ^~~~~~~ 2022-12-17T17:57:19,642 MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’: 2022-12-17T17:57:19,643 MDAnalysis/lib/qcprot.c:2383:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:57:19,643 2383 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2022-12-17T17:57:19,643 | ^ 2022-12-17T17:57:19,646 MDAnalysis/lib/qcprot.c:2591:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:57:19,646 2591 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2022-12-17T17:57:19,646 | ^ 2022-12-17T17:57:25,495 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:57:25,626 building 'MDAnalysis.lib._transformations' extension 2022-12-17T17:57:25,627 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src 2022-12-17T17:57:25,627 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2022-12-17T17:57:25,628 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:57:25,655 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:57:25,970 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:57:25,970 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:57:25,970 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:57:25,970 from MDAnalysis/lib/src/transformations/transformations.c:73: 2022-12-17T17:57:25,971 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:57:25,971 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:57:25,971 | ^~~~~~~ 2022-12-17T17:57:26,035 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: 2022-12-17T17:57:26,035 MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,035 1845 | #pragma vector always 2022-12-17T17:57:26,036 | 2022-12-17T17:57:26,038 MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,038 1962 | #pragma vector always 2022-12-17T17:57:26,038 | 2022-12-17T17:57:26,038 MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,038 1986 | #pragma vector always 2022-12-17T17:57:26,038 | 2022-12-17T17:57:26,042 MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: 2022-12-17T17:57:26,043 MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] 2022-12-17T17:57:26,043 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { 2022-12-17T17:57:26,043 | ^~ 2022-12-17T17:57:26,044 In file included from /usr/include/python3.9/Python.h:97, 2022-12-17T17:57:26,044 from MDAnalysis/lib/src/transformations/transformations.c:68: 2022-12-17T17:57:26,044 /usr/include/python3.9/unicodeobject.h:177:43: note: declared here 2022-12-17T17:57:26,044 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( 2022-12-17T17:57:26,044 | ^~~~~~~~~~~~~~~~~ 2022-12-17T17:57:26,079 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: 2022-12-17T17:57:26,079 MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,080 3427 | #pragma vector always 2022-12-17T17:57:26,080 | 2022-12-17T17:57:26,082 MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,082 3508 | #pragma vector always 2022-12-17T17:57:26,082 | 2022-12-17T17:57:26,087 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: 2022-12-17T17:57:26,088 MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,088 3610 | #pragma vector always 2022-12-17T17:57:26,088 | 2022-12-17T17:57:26,088 MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,088 3615 | #pragma vector always 2022-12-17T17:57:26,088 | 2022-12-17T17:57:26,092 MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,092 3679 | #pragma vector always 2022-12-17T17:57:26,092 | 2022-12-17T17:57:26,092 MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-12-17T17:57:26,093 3684 | #pragma vector always 2022-12-17T17:57:26,093 | 2022-12-17T17:57:26,163 At top level: 2022-12-17T17:57:26,163 MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] 2022-12-17T17:57:26,163 910 | PyConverter_DoubleVector4Copy( 2022-12-17T17:57:26,163 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:57:26,164 MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] 2022-12-17T17:57:26,164 804 | PyConverter_DoubleArrayOrNone( 2022-12-17T17:57:26,164 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:57:26,164 MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] 2022-12-17T17:57:26,164 774 | PyConverter_DoubleArray( 2022-12-17T17:57:26,164 | ^~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:57:31,921 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:57:32,065 building 'MDAnalysis.lib.formats.libmdaxdr' extension 2022-12-17T17:57:32,066 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2022-12-17T17:57:32,067 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:57:32,100 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:57:32,440 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:57:32,440 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:57:32,440 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:57:32,441 from MDAnalysis/lib/formats/libmdaxdr.c:802: 2022-12-17T17:57:32,441 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:57:32,441 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:57:32,441 | ^~~~~~~ 2022-12-17T17:57:32,480 In file included from MDAnalysis/lib/formats/libmdaxdr.c:811: 2022-12-17T17:57:32,480 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:57:32,480 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:57:32,480 | 2022-12-17T17:57:32,482 In file included from MDAnalysis/lib/formats/libmdaxdr.c:812: 2022-12-17T17:57:32,483 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:57:32,483 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:57:32,483 | 2022-12-17T17:57:32,483 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2022-12-17T17:57:32,484 from MDAnalysis/lib/formats/libmdaxdr.c:812: 2022-12-17T17:57:32,484 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:57:32,484 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:57:32,484 | 2022-12-17T17:57:32,485 In file included from MDAnalysis/lib/formats/libmdaxdr.c:813: 2022-12-17T17:57:32,486 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:57:32,486 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:57:32,486 | 2022-12-17T17:58:04,750 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:58:04,779 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:04,874 In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: 2022-12-17T17:58:04,874 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:04,874 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:04,874 | 2022-12-17T17:58:04,880 In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: 2022-12-17T17:58:04,880 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:04,880 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:04,880 | 2022-12-17T17:58:04,881 In file included from /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2022-12-17T17:58:04,881 from MDAnalysis/lib/formats/src/trr_seek.c:31: 2022-12-17T17:58:04,881 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:04,881 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:04,882 | 2022-12-17T17:58:04,885 MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’: 2022-12-17T17:58:04,885 MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable] 2022-12-17T17:58:04,885 39 | int result, framebytes, totalframebytes; 2022-12-17T17:58:04,885 | ^~~~~~~~~~~~~~~ 2022-12-17T17:58:04,886 MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable] 2022-12-17T17:58:04,886 38 | float time, lambda; 2022-12-17T17:58:04,886 | ^~~~~~ 2022-12-17T17:58:04,886 MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable] 2022-12-17T17:58:04,886 38 | float time, lambda; 2022-12-17T17:58:04,886 | ^~~~ 2022-12-17T17:58:05,000 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:58:05,022 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:05,123 In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: 2022-12-17T17:58:05,123 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:05,123 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:05,123 | 2022-12-17T17:58:05,133 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’: 2022-12-17T17:58:05,134 MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-12-17T17:58:05,134 501 | while (size >= num && num_of_bits < 32) 2022-12-17T17:58:05,134 | ^~ 2022-12-17T17:58:05,135 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’: 2022-12-17T17:58:05,135 MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:58:05,135 547 | while (bytes[num_of_bytes] >= num) 2022-12-17T17:58:05,136 | ^~ 2022-12-17T17:58:05,137 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’: 2022-12-17T17:58:05,137 MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-12-17T17:58:05,137 656 | if (num_of_bits >= num_of_bytes * 8) 2022-12-17T17:58:05,138 | ^~ 2022-12-17T17:58:05,138 MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-12-17T17:58:05,138 658 | for (i = 0; i < num_of_bytes; i++) 2022-12-17T17:58:05,138 | ^ 2022-12-17T17:58:05,139 MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-12-17T17:58:05,139 666 | for (i = 0; i < num_of_bytes-1; i++) 2022-12-17T17:58:05,139 | ^ 2022-12-17T17:58:05,140 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’: 2022-12-17T17:58:05,140 MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:58:05,140 706 | if (lastbits < num_of_bits) 2022-12-17T17:58:05,141 | ^ 2022-12-17T17:58:05,142 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2022-12-17T17:58:05,143 MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:58:05,143 816 | if(size3>xfp->buf1size) 2022-12-17T17:58:05,143 | ^ 2022-12-17T17:58:05,145 MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:58:05,145 868 | maxidx = (LASTIDXxfp->buf1size) 2022-12-17T17:58:05,152 | ^ 2022-12-17T17:58:05,156 MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-12-17T17:58:05,156 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2022-12-17T17:58:05,156 | ^ 2022-12-17T17:58:05,157 MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:58:05,157 1141 | maxidx = (LASTIDXxfp->buf1size) 2022-12-17T17:58:05,165 | ^ 2022-12-17T17:58:05,167 MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:58:05,167 1368 | maxidx = (LASTIDXxfp->buf1size) { 2022-12-17T17:58:05,174 | ^ 2022-12-17T17:58:05,180 MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-12-17T17:58:05,180 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2022-12-17T17:58:05,180 | ^ 2022-12-17T17:58:05,181 MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-12-17T17:58:05,181 1624 | maxidx = (LASTIDX maxsize) 2022-12-17T17:58:06,841 | ^ 2022-12-17T17:58:06,842 MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here 2022-12-17T17:58:06,842 2335 | unsigned int size; 2022-12-17T17:58:06,842 | ^~~~ 2022-12-17T17:58:07,273 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2022-12-17T17:58:07,274 MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-12-17T17:58:07,274 1157 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2022-12-17T17:58:07,274 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-12-17T17:58:07,274 MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-12-17T17:58:07,275 1156 | abs(thiscoord[1] - prevcoord[1]) < larger && 2022-12-17T17:58:07,275 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-12-17T17:58:07,275 MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-12-17T17:58:07,275 1155 | abs(thiscoord[0] - prevcoord[0]) < larger && 2022-12-17T17:58:07,275 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-12-17T17:58:08,032 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2022-12-17T17:58:08,033 MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-12-17T17:58:08,033 1639 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2022-12-17T17:58:08,033 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-12-17T17:58:08,034 MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-12-17T17:58:08,034 1638 | abs(thiscoord[1] - prevcoord[1]) < larger && 2022-12-17T17:58:08,034 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-12-17T17:58:08,035 MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-12-17T17:58:08,035 1637 | abs(thiscoord[0] - prevcoord[0]) < larger && 2022-12-17T17:58:08,035 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-12-17T17:58:09,069 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:58:09,095 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:09,147 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: 2022-12-17T17:58:09,147 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:09,147 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:09,147 | 2022-12-17T17:58:09,151 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2022-12-17T17:58:09,152 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:09,152 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:09,152 | 2022-12-17T17:58:09,152 In file included from /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2022-12-17T17:58:09,152 from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2022-12-17T17:58:09,153 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:09,153 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:09,153 | 2022-12-17T17:58:09,154 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’: 2022-12-17T17:58:09,154 MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2022-12-17T17:58:09,154 78 | if (slen != strlen(version) + 1) 2022-12-17T17:58:09,154 | ^~ 2022-12-17T17:58:09,154 MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2022-12-17T17:58:09,155 86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) 2022-12-17T17:58:09,155 | ^~ 2022-12-17T17:58:09,170 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’: 2022-12-17T17:58:09,170 MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized] 2022-12-17T17:58:09,170 408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); 2022-12-17T17:58:09,170 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:10,262 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:58:10,288 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:10,312 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: 2022-12-17T17:58:10,313 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:10,313 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:10,313 | 2022-12-17T17:58:10,324 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2022-12-17T17:58:10,325 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:10,325 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:10,325 | 2022-12-17T17:58:10,325 In file included from /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2022-12-17T17:58:10,325 from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2022-12-17T17:58:10,325 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:10,326 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:10,326 | 2022-12-17T17:58:10,451 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:58:10,478 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:10,502 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: 2022-12-17T17:58:10,502 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:10,502 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:10,502 | 2022-12-17T17:58:10,514 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2022-12-17T17:58:10,514 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:10,514 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:10,514 | 2022-12-17T17:58:10,515 In file included from /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2022-12-17T17:58:10,515 from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2022-12-17T17:58:10,515 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-12-17T17:58:10,515 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-12-17T17:58:10,515 | 2022-12-17T17:58:10,706 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:58:10,954 building 'MDAnalysis.lib.formats.cython_util' extension 2022-12-17T17:58:10,955 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-12-17T17:58:10,987 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:11,300 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:58:11,301 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:58:11,301 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:58:11,301 from MDAnalysis/lib/formats/cython_util.c:775: 2022-12-17T17:58:11,301 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:58:11,301 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:58:11,301 | ^~~~~~~ 2022-12-17T17:58:28,088 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:58:28,258 building 'MDAnalysis.analysis.encore.cutils' extension 2022-12-17T17:58:28,259 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-12-17T17:58:28,260 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-12-17T17:58:28,261 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-12-17T17:58:28,289 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:28,627 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:58:28,628 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:58:28,628 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:58:28,628 from MDAnalysis/analysis/encore/cutils.c:775: 2022-12-17T17:58:28,628 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:58:28,628 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:58:28,628 | ^~~~~~~ 2022-12-17T17:58:31,272 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:58:31,393 building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension 2022-12-17T17:58:31,394 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-12-17T17:58:31,395 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2022-12-17T17:58:31,396 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-12-17T17:58:31,424 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:31,743 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:58:31,743 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:58:31,744 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:58:31,744 from MDAnalysis/analysis/encore/clustering/affinityprop.c:781: 2022-12-17T17:58:31,744 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:58:31,744 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:58:31,744 | ^~~~~~~ 2022-12-17T17:58:42,261 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-12-17T17:58:42,283 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:43,311 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:58:43,453 building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension 2022-12-17T17:58:43,455 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T17:58:43,455 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2022-12-17T17:58:43,457 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-12-17T17:58:43,484 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:44,188 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-12-17T17:58:44,211 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:44,531 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:58:44,531 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:58:44,531 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:58:44,531 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:781: 2022-12-17T17:58:44,532 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:58:44,532 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:58:44,532 | ^~~~~~~ 2022-12-17T17:58:48,995 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:58:49,130 building 'MDAnalysis.lib._cutil' extension 2022-12-17T17:58:49,131 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2022-12-17T17:58:49,158 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:58:49,405 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:58:49,406 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:58:49,406 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:58:49,406 from MDAnalysis/lib/_cutil.cpp:795: 2022-12-17T17:58:49,406 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:58:49,406 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:58:49,406 | ^~~~~~~ 2022-12-17T17:58:52,398 In file included from MDAnalysis/lib/_cutil.cpp:824: 2022-12-17T17:58:52,398 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:827:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,398 827 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,399 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,399 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:791:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,399 791 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,399 | ^~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,399 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:764:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,400 764 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,400 | ^~~~~~~~~~~~~~ 2022-12-17T17:58:52,400 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:689:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,400 689 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,400 | ^~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,400 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:647:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,401 647 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,401 | ^~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,401 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:618:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,401 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,401 | ^~~~~~~~~~~ 2022-12-17T17:58:52,401 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:596:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,402 596 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,402 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,402 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:573:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,402 573 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,402 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,402 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:557:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,403 557 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2022-12-17T17:58:52,403 | ^~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,403 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:505:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,403 505 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2022-12-17T17:58:52,403 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,403 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:472:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,404 472 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2022-12-17T17:58:52,404 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,404 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:448:13: warning: ‘void _calc_self_distance_array(float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,404 448 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2022-12-17T17:58:52,404 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,404 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:424:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,404 424 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2022-12-17T17:58:52,405 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,405 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:399:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,405 399 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2022-12-17T17:58:52,405 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,405 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:381:13: warning: ‘void _calc_distance_array(float (*)[3], uint64_t, float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,405 381 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2022-12-17T17:58:52,406 | ^~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:58:52,406 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:116:13: warning: ‘void _ortho_pbc(float (*)[3], uint64_t, float*)’ defined but not used [-Wunused-function] 2022-12-17T17:58:52,406 116 | static void _ortho_pbc(coordinate* coords, uint64_t numcoords, float* box) 2022-12-17T17:58:52,406 | ^~~~~~~~~~ 2022-12-17T17:59:19,024 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:59:19,398 building 'MDAnalysis.lib._augment' extension 2022-12-17T17:59:19,398 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2022-12-17T17:59:19,431 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:59:19,667 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T17:59:19,668 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T17:59:19,668 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T17:59:19,668 from MDAnalysis/lib/_augment.cpp:790: 2022-12-17T17:59:19,668 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T17:59:19,668 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T17:59:19,669 | ^~~~~~~ 2022-12-17T17:59:45,326 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so 2022-12-17T17:59:45,661 building 'MDAnalysis.lib.nsgrid' extension 2022-12-17T17:59:45,662 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2022-12-17T17:59:45,695 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T17:59:48,116 In file included from MDAnalysis/lib/nsgrid.cpp:791: 2022-12-17T17:59:48,116 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:827:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,116 827 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,116 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,116 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:791:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,117 791 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,117 | ^~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,117 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:764:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,117 764 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,117 | ^~~~~~~~~~~~~~ 2022-12-17T17:59:48,118 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:689:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,118 689 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,118 | ^~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,118 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:647:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,118 647 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,118 | ^~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,119 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:618:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,119 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,119 | ^~~~~~~~~~~ 2022-12-17T17:59:48,119 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:596:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,119 596 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,119 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,119 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:573:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,119 573 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,120 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,120 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:557:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,120 557 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2022-12-17T17:59:48,120 | ^~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,120 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:505:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,120 505 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2022-12-17T17:59:48,120 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,121 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:472:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,121 472 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2022-12-17T17:59:48,121 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,121 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:448:13: warning: ‘void _calc_self_distance_array(float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,121 448 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2022-12-17T17:59:48,121 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,121 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:424:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,122 424 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2022-12-17T17:59:48,122 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,122 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:399:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,122 399 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2022-12-17T17:59:48,122 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T17:59:48,122 /tmp/pip-wheel-70_9h_r1/mdanalysis_441288c465a74ea3b99c52d8ddf9db25/MDAnalysis/lib/include/calc_distances.h:381:13: warning: ‘void _calc_distance_array(float (*)[3], uint64_t, float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-12-17T17:59:48,122 381 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2022-12-17T17:59:48,122 | ^~~~~~~~~~~~~~~~~~~~ 2022-12-17T18:00:10,633 In file included from /usr/include/c++/10/vector:72, 2022-12-17T18:00:10,633 from MDAnalysis/lib/nsgrid.cpp:789: 2022-12-17T18:00:10,633 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2022-12-17T18:00:10,633 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-12-17T18:00:10,633 426 | vector<_Tp, _Alloc>:: 2022-12-17T18:00:10,634 | ^~~~~~~~~~~~~~~~~~~ 2022-12-17T18:00:10,669 In file included from /usr/include/c++/10/vector:67, 2022-12-17T18:00:10,670 from MDAnalysis/lib/nsgrid.cpp:789: 2022-12-17T18:00:10,670 /usr/include/c++/10/bits/stl_vector.h: In function ‘void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_add_neighbors(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, int, int, double)’: 2022-12-17T18:00:10,670 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-12-17T18:00:10,670 1198 | _M_realloc_insert(end(), __x); 2022-12-17T18:00:10,670 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-12-17T18:00:10,707 In file included from /usr/include/c++/10/vector:72, 2022-12-17T18:00:10,707 from MDAnalysis/lib/nsgrid.cpp:789: 2022-12-17T18:00:10,707 /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 = {double}; _Tp = double; _Alloc = std::allocator]’: 2022-12-17T18:00:10,707 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-12-17T18:00:10,707 426 | vector<_Tp, _Alloc>:: 2022-12-17T18:00:10,708 | ^~~~~~~~~~~~~~~~~~~ 2022-12-17T18:00:10,958 /usr/include/c++/10/bits/vector.tcc: In function ‘PyObject* __pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults__set_state(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, PyObject*)’: 2022-12-17T18:00:10,958 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-12-17T18:00:10,958 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-12-17T18:00:10,959 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-12-17T18:00:15,815 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so 2022-12-17T18:00:18,850 building 'MDAnalysis.coordinates.timestep' extension 2022-12-17T18:00:18,851 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-12-17T18:00:18,853 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/tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2022-12-17T18:00:18,892 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-12-17T18:00:19,223 In file included from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2022-12-17T18:00:19,223 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-12-17T18:00:19,224 from /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2022-12-17T18:00:19,224 from MDAnalysis/coordinates/timestep.cpp:791: 2022-12-17T18:00:19,224 /tmp/pip-build-env-m68reu_b/overlay/lib/python3.9/site-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] 2022-12-17T18:00:19,224 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-12-17T18:00:19,224 | ^~~~~~~ 2022-12-17T18:00:37,306 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so 2022-12-17T18:00:37,553 installing to build/bdist.linux-armv7l/wheel 2022-12-17T18:00:37,554 running install 2022-12-17T18:00:37,580 running install_lib 2022-12-17T18:00:37,587 creating build/bdist.linux-armv7l 2022-12-17T18:00:37,588 creating build/bdist.linux-armv7l/wheel 2022-12-17T18:00:37,590 creating build/bdist.linux-armv7l/wheel/MDAnalysis 2022-12-17T18:00:37,592 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-12-17T18:00:37,595 creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-12-17T18:00:37,597 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-12-17T18:00:37,600 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-12-17T18:00:37,604 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-12-17T18:00:37,608 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-12-17T18:00:37,611 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-12-17T18:00:37,614 creating build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,616 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,618 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,624 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,628 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,632 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,640 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,644 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,648 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,651 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/accessors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-12-17T18:00:37,654 creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2022-12-17T18:00:37,656 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2022-12-17T18:00:37,658 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2022-12-17T18:00:37,661 creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,662 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,665 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/wrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,668 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,672 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,675 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,678 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,682 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,685 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-12-17T18:00:37,688 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-12-17T18:00:37,691 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:37,692 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:37,695 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:37,698 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:37,701 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:37,706 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:37,710 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:37,715 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,716 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,718 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,722 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,753 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2022-12-17T18:00:37,754 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2022-12-17T18:00:37,758 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2022-12-17T18:00:37,761 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2022-12-17T18:00:37,764 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2022-12-17T18:00:37,766 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2022-12-17T18:00:37,768 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,770 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,773 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,786 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,826 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,828 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,876 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,899 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,929 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,933 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-12-17T18:00:37,954 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,955 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,958 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,960 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,963 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,966 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,970 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,973 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,976 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2022-12-17T18:00:37,978 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,007 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,049 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src 2022-12-17T18:00:38,051 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2022-12-17T18:00:38,052 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2022-12-17T18:00:38,054 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2022-12-17T18:00:38,057 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2022-12-17T18:00:38,063 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,066 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,069 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,107 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,133 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,136 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,148 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis 2022-12-17T18:00:38,149 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis 2022-12-17T18:00:38,151 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,176 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,188 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,231 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,234 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,237 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,241 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,251 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,259 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,262 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,287 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include 2022-12-17T18:00:38,288 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include 2022-12-17T18:00:38,291 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,295 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,297 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,341 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,344 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,355 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/correlations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-12-17T18:00:38,358 creating build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-12-17T18:00:38,359 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-12-17T18:00:38,373 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-12-17T18:00:38,376 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-12-17T18:00:38,379 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-12-17T18:00:38,382 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-12-17T18:00:38,385 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-12-17T18:00:38,389 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-12-17T18:00:38,392 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,393 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,396 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,399 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2022-12-17T18:00:38,400 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2022-12-17T18:00:38,402 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2022-12-17T18:00:38,404 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,407 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,410 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,413 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,416 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,420 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,422 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/bat.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,425 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,429 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/msd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,432 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,435 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-12-17T18:00:38,436 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-12-17T18:00:38,439 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-12-17T18:00:38,442 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-12-17T18:00:38,445 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-12-17T18:00:38,448 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,451 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,454 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-12-17T18:00:38,455 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-12-17T18:00:38,457 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-12-17T18:00:38,462 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-12-17T18:00:38,465 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-12-17T18:00:38,469 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,472 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,476 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,478 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,482 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-12-17T18:00:38,483 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-12-17T18:00:38,485 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-12-17T18:00:38,488 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-12-17T18:00:38,491 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-12-17T18:00:38,495 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2022-12-17T18:00:38,496 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2022-12-17T18:00:38,499 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2022-12-17T18:00:38,502 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,505 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,508 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,510 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,513 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-12-17T18:00:38,517 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,517 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,520 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,527 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,530 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,537 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,539 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,541 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,544 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,572 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T18:00:38,573 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T18:00:38,575 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T18:00:38,585 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src 2022-12-17T18:00:38,586 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src 2022-12-17T18:00:38,589 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T18:00:38,591 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T18:00:38,604 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T18:00:38,607 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include 2022-12-17T18:00:38,607 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include 2022-12-17T18:00:38,609 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-12-17T18:00:38,630 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-12-17T18:00:38,635 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-12-17T18:00:38,636 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-12-17T18:00:38,638 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-12-17T18:00:38,652 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src 2022-12-17T18:00:38,653 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src 2022-12-17T18:00:38,656 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-12-17T18:00:38,658 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-12-17T18:00:38,660 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-12-17T18:00:38,663 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-12-17T18:00:38,674 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include 2022-12-17T18:00:38,675 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include 2022-12-17T18:00:38,677 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-12-17T18:00:38,681 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,682 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,686 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,688 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,690 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,693 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,696 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,699 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,702 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,705 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,708 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,710 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,713 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,715 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,718 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,720 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,723 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,726 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,731 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,757 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,759 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,761 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,763 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,766 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,768 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,772 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,774 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,776 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,779 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,804 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,806 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,809 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,812 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,815 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,817 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,820 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,823 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,826 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-12-17T18:00:38,829 creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2022-12-17T18:00:38,830 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2022-12-17T18:00:38,833 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2022-12-17T18:00:38,836 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2022-12-17T18:00:38,839 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-12-17T18:00:38,841 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-12-17T18:00:38,844 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,845 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,847 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,850 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-12-17T18:00:38,851 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-12-17T18:00:38,853 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-12-17T18:00:38,856 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-12-17T18:00:38,859 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-12-17T18:00:38,862 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,865 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,868 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,871 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,874 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,877 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,879 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,881 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,884 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,886 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,889 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,892 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,894 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,897 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,900 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,903 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,905 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,907 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,910 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,913 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,915 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,917 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,920 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,923 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,925 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,928 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-12-17T18:00:38,931 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-12-17T18:00:38,934 creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-12-17T18:00:38,979 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-12-17T18:00:38,981 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-12-17T18:00:38,983 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-12-17T18:00:38,985 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-12-17T18:00:38,987 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-12-17T18:00:38,990 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-12-17T18:00:38,993 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-12-17T18:00:38,995 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-12-17T18:00:38,997 running install_egg_info 2022-12-17T18:00:39,005 Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-2.4.1-py3.9.egg-info 2022-12-17T18:00:39,020 running install_scripts 2022-12-17T18:00:39,117 creating build/bdist.linux-armv7l/wheel/MDAnalysis-2.4.1.dist-info/WHEEL 2022-12-17T18:00:39,120 creating '/tmp/pip-wheel-voz9plh5/.tmp-yqejiyna/MDAnalysis-2.4.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-12-17T18:00:39,124 adding 'MDAnalysis/__init__.py' 2022-12-17T18:00:39,125 adding 'MDAnalysis/authors.py' 2022-12-17T18:00:39,127 adding 'MDAnalysis/due.py' 2022-12-17T18:00:39,128 adding 'MDAnalysis/exceptions.py' 2022-12-17T18:00:39,131 adding 'MDAnalysis/units.py' 2022-12-17T18:00:39,133 adding 'MDAnalysis/version.py' 2022-12-17T18:00:39,135 adding 'MDAnalysis/analysis/__init__.py' 2022-12-17T18:00:39,143 adding 'MDAnalysis/analysis/align.py' 2022-12-17T18:00:39,147 adding 'MDAnalysis/analysis/base.py' 2022-12-17T18:00:39,150 adding 'MDAnalysis/analysis/bat.py' 2022-12-17T18:00:39,153 adding 'MDAnalysis/analysis/contacts.py' 2022-12-17T18:00:39,158 adding 'MDAnalysis/analysis/density.py' 2022-12-17T18:00:39,160 adding 'MDAnalysis/analysis/dielectric.py' 2022-12-17T18:00:39,163 adding 'MDAnalysis/analysis/diffusionmap.py' 2022-12-17T18:00:39,166 adding 'MDAnalysis/analysis/dihedrals.py' 2022-12-17T18:00:39,168 adding 'MDAnalysis/analysis/distances.py' 2022-12-17T18:00:39,171 adding 'MDAnalysis/analysis/gnm.py' 2022-12-17T18:00:39,174 adding 'MDAnalysis/analysis/helix_analysis.py' 2022-12-17T18:00:39,176 adding 'MDAnalysis/analysis/leaflet.py' 2022-12-17T18:00:39,179 adding 'MDAnalysis/analysis/lineardensity.py' 2022-12-17T18:00:39,181 adding 'MDAnalysis/analysis/msd.py' 2022-12-17T18:00:39,184 adding 'MDAnalysis/analysis/nucleicacids.py' 2022-12-17T18:00:39,186 adding 'MDAnalysis/analysis/nuclinfo.py' 2022-12-17T18:00:39,191 adding 'MDAnalysis/analysis/pca.py' 2022-12-17T18:00:39,193 adding 'MDAnalysis/analysis/polymer.py' 2022-12-17T18:00:39,203 adding 'MDAnalysis/analysis/psa.py' 2022-12-17T18:00:39,206 adding 'MDAnalysis/analysis/rdf.py' 2022-12-17T18:00:39,211 adding 'MDAnalysis/analysis/rms.py' 2022-12-17T18:00:39,216 adding 'MDAnalysis/analysis/waterdynamics.py' 2022-12-17T18:00:39,218 adding 'MDAnalysis/analysis/data/__init__.py' 2022-12-17T18:00:39,220 adding 'MDAnalysis/analysis/data/filenames.py' 2022-12-17T18:00:39,223 adding 'MDAnalysis/analysis/data/janin_ref_data.npy' 2022-12-17T18:00:39,229 adding 'MDAnalysis/analysis/data/rama_ref_data.npy' 2022-12-17T18:00:39,232 adding 'MDAnalysis/analysis/encore/__init__.py' 2022-12-17T18:00:39,233 adding 'MDAnalysis/analysis/encore/bootstrap.py' 2022-12-17T18:00:39,236 adding 'MDAnalysis/analysis/encore/confdistmatrix.py' 2022-12-17T18:00:39,238 adding 'MDAnalysis/analysis/encore/covariance.py' 2022-12-17T18:00:39,259 adding 'MDAnalysis/analysis/encore/cutils.c' 2022-12-17T18:00:39,296 adding 'MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:39,298 adding 'MDAnalysis/analysis/encore/cutils.pyx' 2022-12-17T18:00:39,305 adding 'MDAnalysis/analysis/encore/similarity.py' 2022-12-17T18:00:39,308 adding 'MDAnalysis/analysis/encore/utils.py' 2022-12-17T18:00:39,311 adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' 2022-12-17T18:00:39,313 adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' 2022-12-17T18:00:39,315 adding 'MDAnalysis/analysis/encore/clustering/__init__.py' 2022-12-17T18:00:39,345 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' 2022-12-17T18:00:39,452 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:39,457 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' 2022-12-17T18:00:39,459 adding 'MDAnalysis/analysis/encore/clustering/cluster.py' 2022-12-17T18:00:39,462 adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' 2022-12-17T18:00:39,464 adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' 2022-12-17T18:00:39,467 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' 2022-12-17T18:00:39,468 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' 2022-12-17T18:00:39,470 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' 2022-12-17T18:00:39,495 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' 2022-12-17T18:00:39,562 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:39,566 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' 2022-12-17T18:00:39,568 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' 2022-12-17T18:00:39,571 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' 2022-12-17T18:00:39,573 adding 'MDAnalysis/analysis/hbonds/__init__.py' 2022-12-17T18:00:39,575 adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' 2022-12-17T18:00:39,578 adding 'MDAnalysis/analysis/hole2/__init__.py' 2022-12-17T18:00:39,584 adding 'MDAnalysis/analysis/hole2/hole.py' 2022-12-17T18:00:39,586 adding 'MDAnalysis/analysis/hole2/templates.py' 2022-12-17T18:00:39,589 adding 'MDAnalysis/analysis/hole2/utils.py' 2022-12-17T18:00:39,591 adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' 2022-12-17T18:00:39,595 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' 2022-12-17T18:00:39,599 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' 2022-12-17T18:00:39,608 adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' 2022-12-17T18:00:39,610 adding 'MDAnalysis/analysis/legacy/__init__.py' 2022-12-17T18:00:39,615 adding 'MDAnalysis/analysis/legacy/x3dna.py' 2022-12-17T18:00:39,618 adding 'MDAnalysis/auxiliary/EDR.py' 2022-12-17T18:00:39,620 adding 'MDAnalysis/auxiliary/XVG.py' 2022-12-17T18:00:39,623 adding 'MDAnalysis/auxiliary/__init__.py' 2022-12-17T18:00:39,629 adding 'MDAnalysis/auxiliary/base.py' 2022-12-17T18:00:39,631 adding 'MDAnalysis/auxiliary/core.py' 2022-12-17T18:00:39,633 adding 'MDAnalysis/converters/OpenMM.py' 2022-12-17T18:00:39,635 adding 'MDAnalysis/converters/OpenMMParser.py' 2022-12-17T18:00:39,638 adding 'MDAnalysis/converters/ParmEd.py' 2022-12-17T18:00:39,640 adding 'MDAnalysis/converters/ParmEdParser.py' 2022-12-17T18:00:39,645 adding 'MDAnalysis/converters/RDKit.py' 2022-12-17T18:00:39,648 adding 'MDAnalysis/converters/RDKitParser.py' 2022-12-17T18:00:39,649 adding 'MDAnalysis/converters/__init__.py' 2022-12-17T18:00:39,652 adding 'MDAnalysis/coordinates/CRD.py' 2022-12-17T18:00:39,655 adding 'MDAnalysis/coordinates/DCD.py' 2022-12-17T18:00:39,657 adding 'MDAnalysis/coordinates/DLPoly.py' 2022-12-17T18:00:39,659 adding 'MDAnalysis/coordinates/DMS.py' 2022-12-17T18:00:39,661 adding 'MDAnalysis/coordinates/FHIAIMS.py' 2022-12-17T18:00:39,663 adding 'MDAnalysis/coordinates/GMS.py' 2022-12-17T18:00:39,666 adding 'MDAnalysis/coordinates/GRO.py' 2022-12-17T18:00:39,668 adding 'MDAnalysis/coordinates/GSD.py' 2022-12-17T18:00:39,675 adding 'MDAnalysis/coordinates/H5MD.py' 2022-12-17T18:00:39,677 adding 'MDAnalysis/coordinates/INPCRD.py' 2022-12-17T18:00:39,681 adding 'MDAnalysis/coordinates/LAMMPS.py' 2022-12-17T18:00:39,682 adding 'MDAnalysis/coordinates/MMTF.py' 2022-12-17T18:00:39,685 adding 'MDAnalysis/coordinates/MOL2.py' 2022-12-17T18:00:39,686 adding 'MDAnalysis/coordinates/NAMDBIN.py' 2022-12-17T18:00:39,693 adding 'MDAnalysis/coordinates/PDB.py' 2022-12-17T18:00:39,696 adding 'MDAnalysis/coordinates/PDBQT.py' 2022-12-17T18:00:39,699 adding 'MDAnalysis/coordinates/PQR.py' 2022-12-17T18:00:39,700 adding 'MDAnalysis/coordinates/ParmEd.py' 2022-12-17T18:00:39,703 adding 'MDAnalysis/coordinates/TNG.py' 2022-12-17T18:00:39,709 adding 'MDAnalysis/coordinates/TRJ.py' 2022-12-17T18:00:39,711 adding 'MDAnalysis/coordinates/TRR.py' 2022-12-17T18:00:39,714 adding 'MDAnalysis/coordinates/TRZ.py' 2022-12-17T18:00:39,716 adding 'MDAnalysis/coordinates/TXYZ.py' 2022-12-17T18:00:39,718 adding 'MDAnalysis/coordinates/XDR.py' 2022-12-17T18:00:39,720 adding 'MDAnalysis/coordinates/XTC.py' 2022-12-17T18:00:39,722 adding 'MDAnalysis/coordinates/XYZ.py' 2022-12-17T18:00:39,727 adding 'MDAnalysis/coordinates/__init__.py' 2022-12-17T18:00:39,735 adding 'MDAnalysis/coordinates/base.py' 2022-12-17T18:00:39,739 adding 'MDAnalysis/coordinates/chain.py' 2022-12-17T18:00:39,743 adding 'MDAnalysis/coordinates/chemfiles.py' 2022-12-17T18:00:39,744 adding 'MDAnalysis/coordinates/core.py' 2022-12-17T18:00:39,748 adding 'MDAnalysis/coordinates/memory.py' 2022-12-17T18:00:39,750 adding 'MDAnalysis/coordinates/null.py' 2022-12-17T18:00:39,808 adding 'MDAnalysis/coordinates/timestep.cpp' 2022-12-17T18:00:40,044 adding 'MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:40,052 adding 'MDAnalysis/coordinates/timestep.pxd' 2022-12-17T18:00:40,056 adding 'MDAnalysis/coordinates/timestep.pyx' 2022-12-17T18:00:40,058 adding 'MDAnalysis/core/__init__.py' 2022-12-17T18:00:40,060 adding 'MDAnalysis/core/_get_readers.py' 2022-12-17T18:00:40,062 adding 'MDAnalysis/core/accessors.py' 2022-12-17T18:00:40,083 adding 'MDAnalysis/core/groups.py' 2022-12-17T18:00:40,091 adding 'MDAnalysis/core/selection.py' 2022-12-17T18:00:40,094 adding 'MDAnalysis/core/topology.py' 2022-12-17T18:00:40,104 adding 'MDAnalysis/core/topologyattrs.py' 2022-12-17T18:00:40,108 adding 'MDAnalysis/core/topologyobjects.py' 2022-12-17T18:00:40,116 adding 'MDAnalysis/core/universe.py' 2022-12-17T18:00:40,120 adding 'MDAnalysis/lib/NeighborSearch.py' 2022-12-17T18:00:40,121 adding 'MDAnalysis/lib/__init__.py' 2022-12-17T18:00:40,196 adding 'MDAnalysis/lib/_augment.cpp' 2022-12-17T18:00:40,470 adding 'MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:40,481 adding 'MDAnalysis/lib/_augment.pyx' 2022-12-17T18:00:40,562 adding 'MDAnalysis/lib/_cutil.cpp' 2022-12-17T18:00:40,912 adding 'MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:40,924 adding 'MDAnalysis/lib/_cutil.pxd' 2022-12-17T18:00:40,927 adding 'MDAnalysis/lib/_cutil.pyx' 2022-12-17T18:00:40,981 adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:41,077 adding 'MDAnalysis/lib/c_distances.c' 2022-12-17T18:00:41,410 adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:41,423 adding 'MDAnalysis/lib/c_distances.pyx' 2022-12-17T18:00:41,447 adding 'MDAnalysis/lib/c_distances_openmp.c' 2022-12-17T18:00:41,508 adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:41,512 adding 'MDAnalysis/lib/c_distances_openmp.pyx' 2022-12-17T18:00:41,514 adding 'MDAnalysis/lib/correlations.py' 2022-12-17T18:00:41,521 adding 'MDAnalysis/lib/distances.py' 2022-12-17T18:00:41,524 adding 'MDAnalysis/lib/log.py' 2022-12-17T18:00:41,526 adding 'MDAnalysis/lib/mdamath.py' 2022-12-17T18:00:41,611 adding 'MDAnalysis/lib/nsgrid.cpp' 2022-12-17T18:00:41,944 adding 'MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:42,023 adding 'MDAnalysis/lib/nsgrid.pyx' 2022-12-17T18:00:42,025 adding 'MDAnalysis/lib/picklable_file_io.py' 2022-12-17T18:00:42,027 adding 'MDAnalysis/lib/pkdtree.py' 2022-12-17T18:00:42,059 adding 'MDAnalysis/lib/qcprot.c' 2022-12-17T18:00:42,135 adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:42,140 adding 'MDAnalysis/lib/qcprot.pyx' 2022-12-17T18:00:42,147 adding 'MDAnalysis/lib/transformations.py' 2022-12-17T18:00:42,159 adding 'MDAnalysis/lib/util.py' 2022-12-17T18:00:42,206 adding 'MDAnalysis/lib/formats/__init__.py' 2022-12-17T18:00:42,274 adding 'MDAnalysis/lib/formats/cython_util.c' 2022-12-17T18:00:42,546 adding 'MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:42,597 adding 'MDAnalysis/lib/formats/cython_util.pxd' 2022-12-17T18:00:42,599 adding 'MDAnalysis/lib/formats/cython_util.pyx' 2022-12-17T18:00:42,697 adding 'MDAnalysis/lib/formats/libdcd.c' 2022-12-17T18:00:43,108 adding 'MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:43,131 adding 'MDAnalysis/lib/formats/libdcd.pxd' 2022-12-17T18:00:43,134 adding 'MDAnalysis/lib/formats/libdcd.pyx' 2022-12-17T18:00:43,232 adding 'MDAnalysis/lib/formats/libmdaxdr.c' 2022-12-17T18:00:43,870 adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so' 2022-12-17T18:00:43,885 adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' 2022-12-17T18:00:43,888 adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' 2022-12-17T18:00:43,922 adding 'MDAnalysis/lib/formats/include/endianswap.h' 2022-12-17T18:00:43,924 adding 'MDAnalysis/lib/formats/include/fastio.h' 2022-12-17T18:00:43,927 adding 'MDAnalysis/lib/formats/include/readdcd.h' 2022-12-17T18:00:43,929 adding 'MDAnalysis/lib/formats/include/trr_seek.h' 2022-12-17T18:00:43,932 adding 'MDAnalysis/lib/formats/include/xdrfile.h' 2022-12-17T18:00:43,948 adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' 2022-12-17T18:00:43,949 adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' 2022-12-17T18:00:43,951 adding 'MDAnalysis/lib/formats/include/xtc_seek.h' 2022-12-17T18:00:43,953 adding 'MDAnalysis/lib/formats/src/trr_seek.c' 2022-12-17T18:00:43,960 adding 'MDAnalysis/lib/formats/src/xdrfile.c' 2022-12-17T18:00:43,963 adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' 2022-12-17T18:00:44,010 adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' 2022-12-17T18:00:44,032 adding 'MDAnalysis/lib/formats/src/xtc_seek.c' 2022-12-17T18:00:44,038 adding 'MDAnalysis/lib/include/calc_distances.h' 2022-12-17T18:00:44,052 adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' 2022-12-17T18:00:44,054 adding 'MDAnalysis/lib/src/transformations/AUTHOR' 2022-12-17T18:00:44,055 adding 'MDAnalysis/lib/src/transformations/LICENCE' 2022-12-17T18:00:44,066 adding 'MDAnalysis/lib/src/transformations/transformations.c' 2022-12-17T18:00:44,068 adding 'MDAnalysis/selections/__init__.py' 2022-12-17T18:00:44,070 adding 'MDAnalysis/selections/base.py' 2022-12-17T18:00:44,072 adding 'MDAnalysis/selections/charmm.py' 2022-12-17T18:00:44,073 adding 'MDAnalysis/selections/gromacs.py' 2022-12-17T18:00:44,075 adding 'MDAnalysis/selections/jmol.py' 2022-12-17T18:00:44,076 adding 'MDAnalysis/selections/pymol.py' 2022-12-17T18:00:44,078 adding 'MDAnalysis/selections/vmd.py' 2022-12-17T18:00:44,080 adding 'MDAnalysis/tests/__init__.py' 2022-12-17T18:00:44,081 adding 'MDAnalysis/tests/datafiles.py' 2022-12-17T18:00:44,084 adding 'MDAnalysis/topology/CRDParser.py' 2022-12-17T18:00:44,085 adding 'MDAnalysis/topology/DLPolyParser.py' 2022-12-17T18:00:44,087 adding 'MDAnalysis/topology/DMSParser.py' 2022-12-17T18:00:44,089 adding 'MDAnalysis/topology/ExtendedPDBParser.py' 2022-12-17T18:00:44,090 adding 'MDAnalysis/topology/FHIAIMSParser.py' 2022-12-17T18:00:44,092 adding 'MDAnalysis/topology/GMSParser.py' 2022-12-17T18:00:44,093 adding 'MDAnalysis/topology/GROParser.py' 2022-12-17T18:00:44,095 adding 'MDAnalysis/topology/GSDParser.py' 2022-12-17T18:00:44,096 adding 'MDAnalysis/topology/HoomdXMLParser.py' 2022-12-17T18:00:44,100 adding 'MDAnalysis/topology/ITPParser.py' 2022-12-17T18:00:44,103 adding 'MDAnalysis/topology/LAMMPSParser.py' 2022-12-17T18:00:44,105 adding 'MDAnalysis/topology/MMTFParser.py' 2022-12-17T18:00:44,107 adding 'MDAnalysis/topology/MOL2Parser.py' 2022-12-17T18:00:44,108 adding 'MDAnalysis/topology/MinimalParser.py' 2022-12-17T18:00:44,111 adding 'MDAnalysis/topology/PDBParser.py' 2022-12-17T18:00:44,112 adding 'MDAnalysis/topology/PDBQTParser.py' 2022-12-17T18:00:44,114 adding 'MDAnalysis/topology/PQRParser.py' 2022-12-17T18:00:44,117 adding 'MDAnalysis/topology/PSFParser.py' 2022-12-17T18:00:44,118 adding 'MDAnalysis/topology/ParmEdParser.py' 2022-12-17T18:00:44,121 adding 'MDAnalysis/topology/TOPParser.py' 2022-12-17T18:00:44,123 adding 'MDAnalysis/topology/TPRParser.py' 2022-12-17T18:00:44,125 adding 'MDAnalysis/topology/TXYZParser.py' 2022-12-17T18:00:44,126 adding 'MDAnalysis/topology/XYZParser.py' 2022-12-17T18:00:44,129 adding 'MDAnalysis/topology/__init__.py' 2022-12-17T18:00:44,131 adding 'MDAnalysis/topology/base.py' 2022-12-17T18:00:44,133 adding 'MDAnalysis/topology/core.py' 2022-12-17T18:00:44,135 adding 'MDAnalysis/topology/guessers.py' 2022-12-17T18:00:44,137 adding 'MDAnalysis/topology/tables.py' 2022-12-17T18:00:44,139 adding 'MDAnalysis/topology/tpr/__init__.py' 2022-12-17T18:00:44,141 adding 'MDAnalysis/topology/tpr/obj.py' 2022-12-17T18:00:44,143 adding 'MDAnalysis/topology/tpr/setting.py' 2022-12-17T18:00:44,147 adding 'MDAnalysis/topology/tpr/utils.py' 2022-12-17T18:00:44,149 adding 'MDAnalysis/transformations/__init__.py' 2022-12-17T18:00:44,151 adding 'MDAnalysis/transformations/base.py' 2022-12-17T18:00:44,153 adding 'MDAnalysis/transformations/boxdimensions.py' 2022-12-17T18:00:44,155 adding 'MDAnalysis/transformations/fit.py' 2022-12-17T18:00:44,156 adding 'MDAnalysis/transformations/positionaveraging.py' 2022-12-17T18:00:44,158 adding 'MDAnalysis/transformations/rotate.py' 2022-12-17T18:00:44,160 adding 'MDAnalysis/transformations/translate.py' 2022-12-17T18:00:44,162 adding 'MDAnalysis/transformations/wrap.py' 2022-12-17T18:00:44,163 adding 'MDAnalysis/visualization/__init__.py' 2022-12-17T18:00:44,166 adding 'MDAnalysis/visualization/streamlines.py' 2022-12-17T18:00:44,169 adding 'MDAnalysis/visualization/streamlines_3D.py' 2022-12-17T18:00:44,173 adding 'MDAnalysis-2.4.1.dist-info/AUTHORS' 2022-12-17T18:00:44,177 adding 'MDAnalysis-2.4.1.dist-info/LICENSE' 2022-12-17T18:00:44,182 adding 'MDAnalysis-2.4.1.dist-info/METADATA' 2022-12-17T18:00:44,183 adding 'MDAnalysis-2.4.1.dist-info/WHEEL' 2022-12-17T18:00:44,184 adding 'MDAnalysis-2.4.1.dist-info/top_level.txt' 2022-12-17T18:00:44,188 adding 'MDAnalysis-2.4.1.dist-info/RECORD' 2022-12-17T18:00:45,718 removing build/bdist.linux-armv7l/wheel 2022-12-17T18:00:46,167 Building wheel for mdanalysis (pyproject.toml): finished with status 'done' 2022-12-17T18:00:46,367 Created wheel for mdanalysis: filename=MDAnalysis-2.4.1-cp39-cp39-linux_armv7l.whl size=7775788 sha256=f6908b1d7ccb4f424abc3a05af2e41727e6d4b0a4fdb40f03dd0286a667f100f 2022-12-17T18:00:46,368 Stored in directory: /tmp/pip-ephem-wheel-cache-50rxvpiw/wheels/91/66/fe/d987254d73caf104a05c92291a3c7cbb50a0a383530c279807 2022-12-17T18:00:46,403 Successfully built mdanalysis 2022-12-17T18:00:46,701 Removed build tracker: '/tmp/pip-build-tracker-gkvo650r'