2023-03-30T02:19:22,276 Created temporary directory: /tmp/pip-ephem-wheel-cache-z5ift2b_ 2023-03-30T02:19:22,279 Created temporary directory: /tmp/pip-build-tracker-1tslz_jx 2023-03-30T02:19:22,279 Initialized build tracking at /tmp/pip-build-tracker-1tslz_jx 2023-03-30T02:19:22,279 Created build tracker: /tmp/pip-build-tracker-1tslz_jx 2023-03-30T02:19:22,279 Entered build tracker: /tmp/pip-build-tracker-1tslz_jx 2023-03-30T02:19:22,280 Created temporary directory: /tmp/pip-wheel-rkwft2xe 2023-03-30T02:19:22,284 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/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) 2023-03-30T02:19:22,412 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) 2023-03-30T02:19:22,412 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) 2023-03-30T02:19:22,412 Skipping link: No binaries permitted for mdanalysis: 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https://files.pythonhosted.org/packages/f1/34/7eedce6129f71fa38fbf9d7fe3a8f366ddee3142afb07113598bf2b66d81/MDAnalysis-2.4.2-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-03-30T02:19:22,414 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/ee/40/20322a888419cc4aeaafa552c51c97c666a46e69c0d130dc5744ec04ae58/MDAnalysis-2.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-03-30T02:19:22,414 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/8b/65/c72765a2a6c73b8e03e114cf7e1661c28df3049adc42e8c75838b48ca083/MDAnalysis-2.4.2-cp311-cp311-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-03-30T02:19:22,415 Skipping link: No binaries permitted for mdanalysis: 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https://files.pythonhosted.org/packages/eb/74/ab6867e602e5fc30f21ee6fe8669f42c4f47b8b7cc0b5686cad60a2ed7be/MDAnalysis-2.4.3-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-03-30T02:19:22,418 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/91/be/9896583934126d2207d79c9fd1bd19918b1652fafb2d09489e7306c5cbc6/MDAnalysis-2.4.3-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-03-30T02:19:22,418 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/27/5c/17e47fa60624834e70c34f4625cd6105d621fc055bc59339173e71450a6e/MDAnalysis-2.4.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-03-30T02:19:22,419 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/01/a9/1851961fb6f7a64d837de8ecbd4548c42e4066b303ac095498169f8c64e9/MDAnalysis-2.4.3-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-03-30T02:19:22,419 Found link https://files.pythonhosted.org/packages/6b/21/c8e7b9655e7819e6e12fd45b35175a13b73262626aefa0a2d1c6766708bc/MDAnalysis-2.4.3.tar.gz (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8), version: 2.4.3 2023-03-30T02:19:22,420 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdanalysis/ 2023-03-30T02:19:22,420 Getting page https://www.piwheels.org/simple/mdanalysis/ 2023-03-30T02:19:22,421 Found index url https://www.piwheels.org/simple 2023-03-30T02:19:22,579 Fetched page https://www.piwheels.org/simple/mdanalysis/ as text/html 2023-03-30T02:19:22,609 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) 2023-03-30T02:19:22,615 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) 2023-03-30T02:19:22,615 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/) 2023-03-30T02:19:22,615 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/) 2023-03-30T02:19:22,616 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp37-cp37m-linux_armv7l.whl#sha256=1368159b6134befa021a6536dcc02e047dc27b4c4672ae7f3b2f8e1559b43f8e (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,616 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp37-cp37m-linux_armv6l.whl#sha256=1368159b6134befa021a6536dcc02e047dc27b4c4672ae7f3b2f8e1559b43f8e (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,616 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp35-cp35m-linux_armv6l.whl#sha256=b669220c967a8cc746ae35c931d22da666f540595d1e9a9c3bb620effa9205b3 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,616 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.2-cp37-cp37m-linux_armv6l.whl#sha256=10a68d03d53e547d0cd2b7be40ec9af8591482bb43aeb5aad582f8a4926205b1 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,620 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.1-cp35-cp35m-linux_armv7l.whl#sha256=813d426b8a410f1c2297d31517407d5684acd025090423a79196237743514a41 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,620 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.1-cp35-cp35m-linux_armv6l.whl#sha256=813d426b8a410f1c2297d31517407d5684acd025090423a79196237743514a41 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,620 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.1-cp37-cp37m-linux_armv7l.whl#sha256=82dd02ba237b4261c0f0d1f180ee08cda6cd1c25871e12db138518ab9f8ca8a6 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,621 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp34-cp34m-linux_armv7l.whl#sha256=2182ab1095b6fb7758816fb8041d325e39216149dd9cc19f98b2394392a14f1b (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,621 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp34-cp34m-linux_armv6l.whl#sha256=2182ab1095b6fb7758816fb8041d325e39216149dd9cc19f98b2394392a14f1b (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,621 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp35-cp35m-linux_armv6l.whl#sha256=426923348f9332d0762be3c94068ab6f54e143815453ae85d2a749e77e4226f7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,622 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp35-cp35m-linux_armv7l.whl#sha256=426923348f9332d0762be3c94068ab6f54e143815453ae85d2a749e77e4226f7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,622 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp37-cp37m-linux_armv7l.whl#sha256=12656c0ac065200b557f80654ef49efaf3e7605ed9abdb94875f64143616f41d (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,622 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp37-cp37m-linux_armv6l.whl#sha256=12656c0ac065200b557f80654ef49efaf3e7605ed9abdb94875f64143616f41d (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,622 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp34-cp34m-linux_armv7l.whl#sha256=9ed92944cd4b3322d05b9a4bb840fe590ed3be07609a93ffb09fe1f760ac363d (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,622 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp34-cp34m-linux_armv6l.whl#sha256=9ed92944cd4b3322d05b9a4bb840fe590ed3be07609a93ffb09fe1f760ac363d (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,622 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp35-cp35m-linux_armv7l.whl#sha256=66b3e7f35c28b424a6ad19307554c223ebc24916dddb557dbd08762989c32119 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,623 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp35-cp35m-linux_armv6l.whl#sha256=66b3e7f35c28b424a6ad19307554c223ebc24916dddb557dbd08762989c32119 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,623 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp37-cp37m-linux_armv6l.whl#sha256=07e291f5c3ee08d16b280c629411107ae1984f33458036e3418429e5f1a33092 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,623 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp37-cp37m-linux_armv7l.whl#sha256=07e291f5c3ee08d16b280c629411107ae1984f33458036e3418429e5f1a33092 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,623 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp37-cp37m-linux_armv7l.whl#sha256=bff2b2b18becae8ee1095f65c6e0d35f33fbc31544d3a12e9ab41bcdb6a775ce (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,623 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp37-cp37m-linux_armv6l.whl#sha256=bff2b2b18becae8ee1095f65c6e0d35f33fbc31544d3a12e9ab41bcdb6a775ce (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,624 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp34-cp34m-linux_armv6l.whl#sha256=ca0488c00e0be959cac05340ae1deb148c2769996e5abb346ad3a7487c2193d1 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,624 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp34-cp34m-linux_armv7l.whl#sha256=ca0488c00e0be959cac05340ae1deb148c2769996e5abb346ad3a7487c2193d1 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,624 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp35-cp35m-linux_armv6l.whl#sha256=58492c63068e648dfb1879b19f1fa55e6e3b9589ee9141eda53c4aed5a915136 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,624 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp35-cp35m-linux_armv7l.whl#sha256=58492c63068e648dfb1879b19f1fa55e6e3b9589ee9141eda53c4aed5a915136 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,624 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp35-cp35m-linux_armv6l.whl#sha256=28e395835220893e8a10d101072b742e6401a4376ddfacc41e30572d8aa6ed65 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,625 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp35-cp35m-linux_armv7l.whl#sha256=28e395835220893e8a10d101072b742e6401a4376ddfacc41e30572d8aa6ed65 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,625 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp34-cp34m-linux_armv6l.whl#sha256=e959b452e988fe4a9b8459143d6a64eef168bc3b9355a04b20ba20c4bb1bf601 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,625 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp34-cp34m-linux_armv7l.whl#sha256=e959b452e988fe4a9b8459143d6a64eef168bc3b9355a04b20ba20c4bb1bf601 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,625 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp34-cp34m-linux_armv6l.whl#sha256=985988f3d88079fe20f14ddee546fbb7b13e2a70dbeb4ac10c0f38f45afa7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,625 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp34-cp34m-linux_armv7l.whl#sha256=985988f3d88079fe20f14ddee546fbb7b13e2a70dbeb4ac10c0f38f45afa7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,626 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp35-cp35m-linux_armv7l.whl#sha256=933bf37f65e3ae59c832a6798365a3da99432510fcfc802e2d6eaa48db3a7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,626 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp35-cp35m-linux_armv6l.whl#sha256=933bf37f65e3ae59c832a6798365a3da99432510fcfc802e2d6eaa48db3a7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,626 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp34-cp34m-linux_armv6l.whl#sha256=34198e0f9e509df1779c2255812cee0f720dc8e989c7d4b7196337f75f1ef51b (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,626 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/) 2023-03-30T02:19:22,626 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/) 2023-03-30T02:19:22,627 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp35-cp35m-linux_armv6l.whl#sha256=032867bf17eecd5fd249607198ad5c191fac901f2856d5a485ffc53a8eb687d4 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,627 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp35-cp35m-linux_armv7l.whl#sha256=04685acd7ab3d9f580c6dccdc18dfa33d89ea596521eede98bef2ec3f8f58af7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,627 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp35-cp35m-linux_armv6l.whl#sha256=04685acd7ab3d9f580c6dccdc18dfa33d89ea596521eede98bef2ec3f8f58af7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,627 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp34-cp34m-linux_armv6l.whl#sha256=30c2bb9cf26e969dbdc8978bd4710e9e8a42ee42ed7c9ad506c63a0855448307 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,627 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/) 2023-03-30T02:19:22,627 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/) 2023-03-30T02:19:22,628 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/) 2023-03-30T02:19:22,628 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/) 2023-03-30T02:19:22,628 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/) 2023-03-30T02:19:22,628 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/) 2023-03-30T02:19:22,628 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/) 2023-03-30T02:19:22,629 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/) 2023-03-30T02:19:22,629 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp37-cp37m-linux_armv7l.whl#sha256=a073eda71f157be82bd9b81ac12793e63834dde1ac9b63ca704668a88b025c1e (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,630 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/) 2023-03-30T02:19:22,630 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/) 2023-03-30T02:19:22,630 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp35-cp35m-linux_armv6l.whl#sha256=28a9bbed8fd84f6ebdf4efb48ef9e2435715169ef7a558ad7f11a33232e83815 (from https://www.piwheels.org/simple/mdanalysis/) 2023-03-30T02:19:22,631 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/) 2023-03-30T02:19:22,631 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/) 2023-03-30T02:19:22,631 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/) 2023-03-30T02:19:22,631 Skipping link: not a file: https://www.piwheels.org/simple/mdanalysis/ 2023-03-30T02:19:22,632 Skipping link: not a file: https://pypi.org/simple/mdanalysis/ 2023-03-30T02:19:22,656 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates 2023-03-30T02:19:22,673 Collecting mdanalysis==2.4.3 2023-03-30T02:19:22,676 Created temporary directory: /tmp/pip-unpack-vemdxo59 2023-03-30T02:19:23,344 Downloading MDAnalysis-2.4.3.tar.gz (3.7 MB) 2023-03-30T02:19:26,211 Added mdanalysis==2.4.3 from https://files.pythonhosted.org/packages/6b/21/c8e7b9655e7819e6e12fd45b35175a13b73262626aefa0a2d1c6766708bc/MDAnalysis-2.4.3.tar.gz to build tracker '/tmp/pip-build-tracker-1tslz_jx' 2023-03-30T02:19:26,262 Created temporary directory: /tmp/pip-build-env-0gfbkp6c 2023-03-30T02:19:26,273 Installing build dependencies: started 2023-03-30T02:19:26,274 Running command pip subprocess to install build dependencies 2023-03-30T02:19:27,559 Using pip 23.0.1 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2023-03-30T02:19:28,215 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 2023-03-30T02:19:28,311 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-03-30T02:19:28,313 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 2023-03-30T02:19:28,314 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 2023-03-30T02:19:28,315 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 2023-03-30T02:19:28,316 Ignoring numpy: markers 'python_version == "3.10" and platform_system == "Windows" and platform_python_implementation != "PyPy"' don't match your environment 2023-03-30T02:19:28,318 Ignoring numpy: markers 'python_version == "3.10" and platform_system != "Windows" and platform_python_implementation != "PyPy"' don't match your environment 2023-03-30T02:19:28,319 Ignoring numpy: markers 'python_version == "3.11" and platform_python_implementation != "PyPy"' don't match your environment 2023-03-30T02:19:28,320 Ignoring numpy: markers 'python_version >= "3.12"' don't match your environment 2023-03-30T02:19:29,950 Collecting Cython>=0.28 2023-03-30T02:19:30,484 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.33-cp39-cp39-linux_armv7l.whl (5.0 MB) 2023-03-30T02:19:30,834 Collecting packaging 2023-03-30T02:19:30,873 Using cached https://www.piwheels.org/simple/packaging/packaging-23.0-py3-none-any.whl (42 kB) 2023-03-30T02:19:32,105 Collecting numpy==1.20.0 2023-03-30T02:19:32,163 Downloading https://www.piwheels.org/simple/numpy/numpy-1.20.0-cp39-cp39-linux_armv7l.whl (11.6 MB) 2023-03-30T02:19:33,158 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 11.0 MB/s eta 0:00:00 2023-03-30T02:19:34,890 Collecting setuptools 2023-03-30T02:19:35,001 Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.6.1-py3-none-any.whl (1.1 MB) 2023-03-30T02:19:35,322 Collecting wheel 2023-03-30T02:19:35,345 Using cached https://www.piwheels.org/simple/wheel/wheel-0.40.0-py3-none-any.whl (64 kB) 2023-03-30T02:19:37,594 Installing collected packages: wheel, setuptools, packaging, numpy, Cython 2023-03-30T02:19:37,836 Creating /tmp/pip-build-env-0gfbkp6c/overlay/bin 2023-03-30T02:19:37,838 changing mode of /tmp/pip-build-env-0gfbkp6c/overlay/bin/wheel to 755 2023-03-30T02:19:47,722 changing mode of /tmp/pip-build-env-0gfbkp6c/overlay/bin/f2py to 755 2023-03-30T02:19:47,725 changing mode of /tmp/pip-build-env-0gfbkp6c/overlay/bin/f2py3 to 755 2023-03-30T02:19:47,727 changing mode of /tmp/pip-build-env-0gfbkp6c/overlay/bin/f2py3.9 to 755 2023-03-30T02:19:50,576 changing mode of /tmp/pip-build-env-0gfbkp6c/overlay/bin/cygdb to 755 2023-03-30T02:19:50,578 changing mode of /tmp/pip-build-env-0gfbkp6c/overlay/bin/cython to 755 2023-03-30T02:19:50,581 changing mode of /tmp/pip-build-env-0gfbkp6c/overlay/bin/cythonize to 755 2023-03-30T02:19:50,607 Successfully installed Cython-0.29.33 numpy-1.20.0 packaging-23.0 setuptools-67.6.1 wheel-0.40.0 2023-03-30T02:19:51,235 Installing build dependencies: finished with status 'done' 2023-03-30T02:19:51,248 Getting requirements to build wheel: started 2023-03-30T02:19:51,249 Running command Getting requirements to build wheel 2023-03-30T02:20:27,486 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-03-30T02:20:27,486 Will attempt to use Cython. 2023-03-30T02:20:27,487 Compiling MDAnalysis/lib/formats/libdcd.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,487 Compiling MDAnalysis/lib/c_distances.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,487 Compiling MDAnalysis/lib/c_distances_openmp.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,487 Compiling MDAnalysis/lib/qcprot.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,487 Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,487 Compiling MDAnalysis/lib/formats/cython_util.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,488 Compiling MDAnalysis/analysis/encore/cutils.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,488 Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,488 Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-03-30T02:20:27,488 Compiling MDAnalysis/lib/_cutil.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-03-30T02:20:27,488 Compiling MDAnalysis/lib/_augment.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-03-30T02:20:27,488 Compiling MDAnalysis/lib/nsgrid.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-03-30T02:20:27,489 Compiling MDAnalysis/coordinates/timestep.pyx because it depends on /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/__init__.pxd. 2023-03-30T02:20:27,489 [ 1/13] Cythonizing MDAnalysis/lib/_augment.pyx 2023-03-30T02:20:27,489 [ 2/13] Cythonizing MDAnalysis/lib/_cutil.pyx 2023-03-30T02:20:27,489 [ 3/13] Cythonizing MDAnalysis/lib/nsgrid.pyx 2023-03-30T02:20:27,489 [ 4/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx 2023-03-30T02:20:27,489 [ 5/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx 2023-03-30T02:20:27,489 [ 6/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx 2023-03-30T02:20:27,490 [ 7/13] Cythonizing MDAnalysis/coordinates/timestep.pyx 2023-03-30T02:20:27,490 [ 8/13] Cythonizing MDAnalysis/lib/c_distances.pyx 2023-03-30T02:20:27,490 [ 9/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx 2023-03-30T02:20:27,490 [10/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx 2023-03-30T02:20:27,490 [11/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx 2023-03-30T02:20:27,490 [12/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx 2023-03-30T02:20:27,490 [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx 2023-03-30T02:20:28,358 Getting requirements to build wheel: finished with status 'done' 2023-03-30T02:20:28,373 Created temporary directory: /tmp/pip-modern-metadata-rakjdkwr 2023-03-30T02:20:28,376 Preparing metadata (pyproject.toml): started 2023-03-30T02:20:28,377 Running command Preparing metadata (pyproject.toml) 2023-03-30T02:20:30,368 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-03-30T02:20:30,368 Will attempt to use Cython. 2023-03-30T02:20:30,496 /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-03-30T02:20:30,496 warnings.warn(msg) 2023-03-30T02:20:30,810 running dist_info 2023-03-30T02:20:30,817 creating /tmp/pip-modern-metadata-rakjdkwr/MDAnalysis.egg-info 2023-03-30T02:20:30,823 writing /tmp/pip-modern-metadata-rakjdkwr/MDAnalysis.egg-info/PKG-INFO 2023-03-30T02:20:30,828 writing dependency_links to /tmp/pip-modern-metadata-rakjdkwr/MDAnalysis.egg-info/dependency_links.txt 2023-03-30T02:20:30,830 writing requirements to /tmp/pip-modern-metadata-rakjdkwr/MDAnalysis.egg-info/requires.txt 2023-03-30T02:20:30,831 writing top-level names to /tmp/pip-modern-metadata-rakjdkwr/MDAnalysis.egg-info/top_level.txt 2023-03-30T02:20:30,833 writing manifest file '/tmp/pip-modern-metadata-rakjdkwr/MDAnalysis.egg-info/SOURCES.txt' 2023-03-30T02:20:30,880 reading manifest file '/tmp/pip-modern-metadata-rakjdkwr/MDAnalysis.egg-info/SOURCES.txt' 2023-03-30T02:20:30,882 reading manifest template 'MANIFEST.in' 2023-03-30T02:20:31,044 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2023-03-30T02:20:31,046 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-03-30T02:20:31,047 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2023-03-30T02:20:31,049 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2023-03-30T02:20:31,051 warning: no previously-included files matching '*~' found anywhere in distribution 2023-03-30T02:20:31,052 warning: no previously-included files matching '.git' found anywhere in distribution 2023-03-30T02:20:31,052 adding license file 'LICENSE' 2023-03-30T02:20:31,052 adding license file 'AUTHORS' 2023-03-30T02:20:31,070 writing manifest file '/tmp/pip-modern-metadata-rakjdkwr/MDAnalysis.egg-info/SOURCES.txt' 2023-03-30T02:20:31,072 creating '/tmp/pip-modern-metadata-rakjdkwr/MDAnalysis-2.4.3.dist-info' 2023-03-30T02:20:31,307 Preparing metadata (pyproject.toml): finished with status 'done' 2023-03-30T02:20:31,318 Source in /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d has version 2.4.3, which satisfies requirement mdanalysis==2.4.3 from https://files.pythonhosted.org/packages/6b/21/c8e7b9655e7819e6e12fd45b35175a13b73262626aefa0a2d1c6766708bc/MDAnalysis-2.4.3.tar.gz 2023-03-30T02:20:31,319 Removed mdanalysis==2.4.3 from https://files.pythonhosted.org/packages/6b/21/c8e7b9655e7819e6e12fd45b35175a13b73262626aefa0a2d1c6766708bc/MDAnalysis-2.4.3.tar.gz from build tracker '/tmp/pip-build-tracker-1tslz_jx' 2023-03-30T02:20:31,329 Created temporary directory: /tmp/pip-unpack-tvkf4lbp 2023-03-30T02:20:31,330 Building wheels for collected packages: mdanalysis 2023-03-30T02:20:31,334 Created temporary directory: /tmp/pip-wheel-s0rqv8fr 2023-03-30T02:20:31,335 Destination directory: /tmp/pip-wheel-s0rqv8fr 2023-03-30T02:20:31,337 Building wheel for mdanalysis (pyproject.toml): started 2023-03-30T02:20:31,338 Running command Building wheel for mdanalysis (pyproject.toml) 2023-03-30T02:20:33,189 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-03-30T02:20:33,190 Will attempt to use Cython. 2023-03-30T02:20:33,309 /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:203: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-03-30T02:20:33,309 warnings.warn(msg) 2023-03-30T02:20:33,622 running bdist_wheel 2023-03-30T02:20:33,643 running build 2023-03-30T02:20:33,643 running build_py 2023-03-30T02:20:33,650 creating build 2023-03-30T02:20:33,651 creating build/lib.linux-armv7l-cpython-39 2023-03-30T02:20:33,652 creating build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-03-30T02:20:33,653 copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-03-30T02:20:33,656 copying MDAnalysis/units.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-03-30T02:20:33,658 copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-03-30T02:20:33,661 copying MDAnalysis/authors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-03-30T02:20:33,663 copying MDAnalysis/due.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-03-30T02:20:33,665 copying MDAnalysis/version.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-03-30T02:20:33,668 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-03-30T02:20:33,669 copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-03-30T02:20:33,671 copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-03-30T02:20:33,674 copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-03-30T02:20:33,676 copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-03-30T02:20:33,679 copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-03-30T02:20:33,681 copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-03-30T02:20:33,683 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-03-30T02:20:33,686 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,687 copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,691 copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,698 copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,701 copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,703 copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,706 copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,711 copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,714 copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,718 copying MDAnalysis/core/accessors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-03-30T02:20:33,721 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-03-30T02:20:33,722 copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-03-30T02:20:33,725 copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-03-30T02:20:33,728 copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-03-30T02:20:33,731 copying MDAnalysis/converters/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-03-30T02:20:33,733 copying MDAnalysis/converters/RDKit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-03-30T02:20:33,737 copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-03-30T02:20:33,740 copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-03-30T02:20:33,743 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,744 copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,748 copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,751 copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,756 copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,759 copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,762 copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,767 copying MDAnalysis/lib/correlations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,770 copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,772 copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,775 copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:33,781 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-03-30T02:20:33,782 copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-03-30T02:20:33,785 copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-03-30T02:20:33,788 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-03-30T02:20:33,793 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,794 copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,797 copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,800 copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,803 copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,806 copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,809 copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,811 copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,813 copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,815 copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,817 copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,821 copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,823 copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,827 copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,830 copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,832 copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,835 copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,838 copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,840 copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,843 copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,846 copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,848 copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,851 copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,854 copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,856 copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,859 copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,862 copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,864 copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,867 copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-03-30T02:20:33,870 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,871 copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,873 copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,876 copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,879 copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,881 copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,884 copying MDAnalysis/transformations/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,886 copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,889 copying MDAnalysis/transformations/wrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-03-30T02:20:33,892 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-03-30T02:20:33,893 copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-03-30T02:20:33,895 copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-03-30T02:20:33,898 copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-03-30T02:20:33,901 copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-03-30T02:20:33,905 copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-03-30T02:20:33,908 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-03-30T02:20:33,909 copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-03-30T02:20:33,911 copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-03-30T02:20:33,915 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,916 copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,922 copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,925 copying MDAnalysis/analysis/msd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,929 copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,931 copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,935 copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,938 copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,941 copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,944 copying MDAnalysis/analysis/bat.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,947 copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,951 copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,955 copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,957 copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,960 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,962 copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,965 copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,968 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,971 copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,974 copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,978 copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,982 copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,985 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,987 copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:20:33,992 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:33,994 copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:33,996 copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:33,999 copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,001 copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,004 copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,007 copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,009 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,012 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,014 copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,017 copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,020 copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,023 copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,025 copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,028 copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,030 copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,034 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,037 copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,041 copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,044 copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,048 copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,051 copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,054 copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,057 copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,060 copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,063 copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,065 copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,067 copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,070 copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,073 copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,076 copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,079 copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,082 copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,084 copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,087 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,088 copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,091 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-03-30T02:20:34,092 copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-03-30T02:20:34,095 copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-03-30T02:20:34,098 copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-03-30T02:20:34,100 copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-03-30T02:20:34,103 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-03-30T02:20:34,104 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-03-30T02:20:34,107 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-03-30T02:20:34,110 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-03-30T02:20:34,112 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-03-30T02:20:34,117 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:20:34,118 copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:20:34,124 copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:20:34,126 copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:20:34,129 copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:20:34,133 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-03-30T02:20:34,134 copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-03-30T02:20:34,139 copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-03-30T02:20:34,141 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-03-30T02:20:34,142 copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-03-30T02:20:34,146 copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-03-30T02:20:34,149 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,150 copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,154 copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,157 copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,159 copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,162 copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,164 copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,168 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-03-30T02:20:34,169 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-03-30T02:20:34,171 copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-03-30T02:20:34,173 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:20:34,175 copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:20:34,177 copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:20:34,180 copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:20:34,182 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-03-30T02:20:34,183 copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-03-30T02:20:34,185 copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-03-30T02:20:34,188 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-03-30T02:20:34,191 copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-03-30T02:20:34,193 running egg_info 2023-03-30T02:20:34,207 writing MDAnalysis.egg-info/PKG-INFO 2023-03-30T02:20:34,210 writing dependency_links to MDAnalysis.egg-info/dependency_links.txt 2023-03-30T02:20:34,212 writing requirements to MDAnalysis.egg-info/requires.txt 2023-03-30T02:20:34,214 writing top-level names to MDAnalysis.egg-info/top_level.txt 2023-03-30T02:20:34,249 reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2023-03-30T02:20:34,262 reading manifest template 'MANIFEST.in' 2023-03-30T02:20:34,451 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2023-03-30T02:20:34,454 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-03-30T02:20:34,456 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2023-03-30T02:20:34,458 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2023-03-30T02:20:34,461 warning: no previously-included files matching '*~' found anywhere in distribution 2023-03-30T02:20:34,463 warning: no previously-included files matching '.git' found anywhere in distribution 2023-03-30T02:20:34,463 adding license file 'LICENSE' 2023-03-30T02:20:34,463 adding license file 'AUTHORS' 2023-03-30T02:20:34,488 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2023-03-30T02:20:34,492 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,492 !! 2023-03-30T02:20:34,492 ############################ 2023-03-30T02:20:34,492 # Package would be ignored # 2023-03-30T02:20:34,493 ############################ 2023-03-30T02:20:34,493 Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package, 2023-03-30T02:20:34,493 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,493 'MDAnalysis.analysis.encore.clustering.include' has been automatically added to the distribution only 2023-03-30T02:20:34,493 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,493 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,493 Please make sure that 'MDAnalysis.analysis.encore.clustering.include' is included as a package by using 2023-03-30T02:20:34,494 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,494 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,494 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,494 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,494 documentation page. 2023-03-30T02:20:34,495 !! 2023-03-30T02:20:34,495 check.warn(importable) 2023-03-30T02:20:34,495 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,495 !! 2023-03-30T02:20:34,495 ############################ 2023-03-30T02:20:34,496 # Package would be ignored # 2023-03-30T02:20:34,496 ############################ 2023-03-30T02:20:34,496 Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package, 2023-03-30T02:20:34,496 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,496 'MDAnalysis.analysis.encore.clustering.src' has been automatically added to the distribution only 2023-03-30T02:20:34,496 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,496 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,497 Please make sure that 'MDAnalysis.analysis.encore.clustering.src' is included as a package by using 2023-03-30T02:20:34,497 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,497 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,497 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,497 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,497 documentation page. 2023-03-30T02:20:34,498 !! 2023-03-30T02:20:34,498 check.warn(importable) 2023-03-30T02:20:34,498 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,498 !! 2023-03-30T02:20:34,499 ############################ 2023-03-30T02:20:34,499 # Package would be ignored # 2023-03-30T02:20:34,499 ############################ 2023-03-30T02:20:34,499 Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package, 2023-03-30T02:20:34,499 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,499 'MDAnalysis.analysis.encore.dimensionality_reduction.include' has been automatically added to the distribution only 2023-03-30T02:20:34,500 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,500 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,500 Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is included as a package by using 2023-03-30T02:20:34,500 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,500 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,500 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,500 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,501 documentation page. 2023-03-30T02:20:34,501 !! 2023-03-30T02:20:34,501 check.warn(importable) 2023-03-30T02:20:34,501 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,501 !! 2023-03-30T02:20:34,502 ############################ 2023-03-30T02:20:34,502 # Package would be ignored # 2023-03-30T02:20:34,502 ############################ 2023-03-30T02:20:34,502 Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package, 2023-03-30T02:20:34,502 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,502 'MDAnalysis.analysis.encore.dimensionality_reduction.src' has been automatically added to the distribution only 2023-03-30T02:20:34,502 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,503 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,503 Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is included as a package by using 2023-03-30T02:20:34,503 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,503 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,503 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,503 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,503 documentation page. 2023-03-30T02:20:34,504 !! 2023-03-30T02:20:34,504 check.warn(importable) 2023-03-30T02:20:34,504 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,504 !! 2023-03-30T02:20:34,505 ############################ 2023-03-30T02:20:34,505 # Package would be ignored # 2023-03-30T02:20:34,505 ############################ 2023-03-30T02:20:34,505 Python recognizes 'MDAnalysis.lib.formats.include' as an importable package, 2023-03-30T02:20:34,505 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,505 'MDAnalysis.lib.formats.include' has been automatically added to the distribution only 2023-03-30T02:20:34,505 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,505 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,506 Please make sure that 'MDAnalysis.lib.formats.include' is included as a package by using 2023-03-30T02:20:34,506 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,506 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,506 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,506 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,506 documentation page. 2023-03-30T02:20:34,507 !! 2023-03-30T02:20:34,507 check.warn(importable) 2023-03-30T02:20:34,507 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,507 !! 2023-03-30T02:20:34,508 ############################ 2023-03-30T02:20:34,508 # Package would be ignored # 2023-03-30T02:20:34,508 ############################ 2023-03-30T02:20:34,508 Python recognizes 'MDAnalysis.lib.formats.src' as an importable package, 2023-03-30T02:20:34,508 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,508 'MDAnalysis.lib.formats.src' has been automatically added to the distribution only 2023-03-30T02:20:34,508 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,508 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,509 Please make sure that 'MDAnalysis.lib.formats.src' is included as a package by using 2023-03-30T02:20:34,509 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,509 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,509 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,509 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,509 documentation page. 2023-03-30T02:20:34,510 !! 2023-03-30T02:20:34,510 check.warn(importable) 2023-03-30T02:20:34,510 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,510 !! 2023-03-30T02:20:34,510 ############################ 2023-03-30T02:20:34,511 # Package would be ignored # 2023-03-30T02:20:34,511 ############################ 2023-03-30T02:20:34,511 Python recognizes 'MDAnalysis.lib.include' as an importable package, 2023-03-30T02:20:34,511 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,511 'MDAnalysis.lib.include' has been automatically added to the distribution only 2023-03-30T02:20:34,511 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,511 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,512 Please make sure that 'MDAnalysis.lib.include' is included as a package by using 2023-03-30T02:20:34,512 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,512 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,512 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,512 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,512 documentation page. 2023-03-30T02:20:34,513 !! 2023-03-30T02:20:34,513 check.warn(importable) 2023-03-30T02:20:34,513 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,513 !! 2023-03-30T02:20:34,514 ############################ 2023-03-30T02:20:34,514 # Package would be ignored # 2023-03-30T02:20:34,514 ############################ 2023-03-30T02:20:34,514 Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package, 2023-03-30T02:20:34,514 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,514 'MDAnalysis.lib.libmdanalysis' has been automatically added to the distribution only 2023-03-30T02:20:34,514 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,514 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,515 Please make sure that 'MDAnalysis.lib.libmdanalysis' is included as a package by using 2023-03-30T02:20:34,515 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,515 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,515 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,515 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,515 documentation page. 2023-03-30T02:20:34,516 !! 2023-03-30T02:20:34,516 check.warn(importable) 2023-03-30T02:20:34,516 /tmp/pip-build-env-0gfbkp6c/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`. 2023-03-30T02:20:34,516 !! 2023-03-30T02:20:34,517 ############################ 2023-03-30T02:20:34,517 # Package would be ignored # 2023-03-30T02:20:34,517 ############################ 2023-03-30T02:20:34,517 Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package, 2023-03-30T02:20:34,517 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T02:20:34,517 'MDAnalysis.lib.src.transformations' has been automatically added to the distribution only 2023-03-30T02:20:34,517 because it may contain data files, but this behavior is likely to change 2023-03-30T02:20:34,518 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T02:20:34,518 Please make sure that 'MDAnalysis.lib.src.transformations' is included as a package by using 2023-03-30T02:20:34,518 the `packages` configuration field or the proper discovery methods 2023-03-30T02:20:34,518 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T02:20:34,518 instead of `find_packages(...)`/`find:`). 2023-03-30T02:20:34,519 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T02:20:34,519 documentation page. 2023-03-30T02:20:34,520 !! 2023-03-30T02:20:34,520 check.warn(importable) 2023-03-30T02:20:34,520 copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-03-30T02:20:34,521 copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-03-30T02:20:34,525 copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,551 copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,554 copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,583 copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,585 copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,588 copying MDAnalysis/lib/c_distances.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,622 copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,625 copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,637 copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,640 copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,668 copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,671 copying MDAnalysis/lib/qcprot.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,685 copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,688 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include 2023-03-30T02:20:34,689 copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include 2023-03-30T02:20:34,692 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis 2023-03-30T02:20:34,693 copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis 2023-03-30T02:20:34,695 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src 2023-03-30T02:20:34,696 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-03-30T02:20:34,697 copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-03-30T02:20:34,700 copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-03-30T02:20:34,702 copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-03-30T02:20:34,708 copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,735 copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,737 copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:20:34,741 copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,761 copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,763 copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,765 copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,800 copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,802 copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,805 copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,836 copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,839 copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,842 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,843 copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,846 copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,849 copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,852 copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,855 copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,858 copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,860 copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,862 copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-03-30T02:20:34,865 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-03-30T02:20:34,866 copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-03-30T02:20:34,868 copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-03-30T02:20:34,872 copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-03-30T02:20:34,875 copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-03-30T02:20:34,878 copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-03-30T02:20:34,881 copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,891 copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:20:34,893 copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:20:34,905 copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:20:34,907 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-03-30T02:20:34,908 copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-03-30T02:20:34,910 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-03-30T02:20:34,911 copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-03-30T02:20:34,914 copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-03-30T02:20:34,924 copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-03-30T02:20:34,927 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include 2023-03-30T02:20:34,928 copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include 2023-03-30T02:20:34,930 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-03-30T02:20:34,931 copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-03-30T02:20:34,950 running build_ext 2023-03-30T02:20:34,951 building 'MDAnalysis.lib.formats.libdcd' extension 2023-03-30T02:20:34,952 creating build/temp.linux-armv7l-cpython-39 2023-03-30T02:20:34,952 creating build/temp.linux-armv7l-cpython-39/MDAnalysis 2023-03-30T02:20:34,953 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib 2023-03-30T02:20:34,954 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-03-30T02:20:34,955 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-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats -I/tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:20:34,988 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:20:35,495 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:20:35,496 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:20:35,496 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:20:35,496 from MDAnalysis/lib/formats/libdcd.c:781: 2023-03-30T02:20:35,496 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:20:35,496 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:20:35,496 | ^~~~~~~ 2023-03-30T02:20:35,578 In file included from MDAnalysis/lib/formats/libdcd.c:791: 2023-03-30T02:20:35,578 MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’: 2023-03-30T02:20:35,579 MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-03-30T02:20:35,579 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2023-03-30T02:20:35,579 | ^~ 2023-03-30T02:20:35,584 MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’: 2023-03-30T02:20:35,585 MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable] 2023-03-30T02:20:35,585 698 | struct tm *tmbuf; 2023-03-30T02:20:35,585 | ^~~~~ 2023-03-30T02:20:35,586 MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable] 2023-03-30T02:20:35,586 697 | time_t cur_time; 2023-03-30T02:20:35,586 | ^~~~~~~~ 2023-03-30T02:20:37,343 In file included from MDAnalysis/lib/formats/include/readdcd.h:25, 2023-03-30T02:20:37,343 from MDAnalysis/lib/formats/libdcd.c:791: 2023-03-30T02:20:37,343 At top level: 2023-03-30T02:20:37,344 MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2023-03-30T02:20:37,344 96 | static void swap2_aligned(void *v, long ndata) { 2023-03-30T02:20:37,345 | ^~~~~~~~~~~~~ 2023-03-30T02:20:37,345 MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2023-03-30T02:20:37,345 32 | static void swap2_unaligned(void *v, long ndata) { 2023-03-30T02:20:37,345 | ^~~~~~~~~~~~~~~ 2023-03-30T02:20:37,345 In file included from MDAnalysis/lib/formats/libdcd.c:790: 2023-03-30T02:20:37,346 MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2023-03-30T02:20:37,346 453 | static int fio_write_str(fio_fd fd, const char *str) { 2023-03-30T02:20:37,346 | ^~~~~~~~~~~~~ 2023-03-30T02:20:37,346 MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2023-03-30T02:20:37,346 449 | static int fio_read_int32(fio_fd fd, int *i) { 2023-03-30T02:20:37,346 | ^~~~~~~~~~~~~~ 2023-03-30T02:21:08,151 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 2023-03-30T02:21:08,376 building 'MDAnalysis.lib.c_distances' extension 2023-03-30T02:21:08,377 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-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:21:08,412 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:21:08,722 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:21:08,722 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:21:08,722 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:21:08,722 from MDAnalysis/lib/c_distances.c:781: 2023-03-30T02:21:08,722 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:21:08,723 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:21:08,723 | ^~~~~~~ 2023-03-30T02:21:38,942 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 2023-03-30T02:21:39,166 building 'MDAnalysis.lib.c_distances_openmp' extension 2023-03-30T02:21:39,167 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-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:21:39,197 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:21:39,507 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:21:39,508 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:21:39,508 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:21:39,508 from MDAnalysis/lib/c_distances_openmp.c:792: 2023-03-30T02:21:39,508 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:21:39,508 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:21:39,508 | ^~~~~~~ 2023-03-30T02:21:45,287 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 2023-03-30T02:21:45,442 building 'MDAnalysis.lib.qcprot' extension 2023-03-30T02:21:45,443 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-0gfbkp6c/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 2023-03-30T02:21:45,472 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:21:45,774 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:21:45,774 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:21:45,774 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:21:45,775 from MDAnalysis/lib/qcprot.c:775: 2023-03-30T02:21:45,775 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:21:45,775 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:21:45,775 | ^~~~~~~ 2023-03-30T02:21:45,833 MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’: 2023-03-30T02:21:45,833 MDAnalysis/lib/qcprot.c:2383:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:21:45,834 2383 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2023-03-30T02:21:45,834 | ^ 2023-03-30T02:21:45,837 MDAnalysis/lib/qcprot.c:2591:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:21:45,837 2591 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2023-03-30T02:21:45,837 | ^ 2023-03-30T02:21:51,717 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 2023-03-30T02:21:51,845 building 'MDAnalysis.lib._transformations' extension 2023-03-30T02:21:51,846 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src 2023-03-30T02:21:51,847 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-03-30T02:21:51,848 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-0gfbkp6c/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 2023-03-30T02:21:51,876 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:21:52,188 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:21:52,188 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:21:52,188 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:21:52,188 from MDAnalysis/lib/src/transformations/transformations.c:73: 2023-03-30T02:21:52,188 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:21:52,189 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:21:52,189 | ^~~~~~~ 2023-03-30T02:21:52,256 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: 2023-03-30T02:21:52,256 MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,256 1845 | #pragma vector always 2023-03-30T02:21:52,256 | 2023-03-30T02:21:52,258 MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,259 1962 | #pragma vector always 2023-03-30T02:21:52,259 | 2023-03-30T02:21:52,259 MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,259 1986 | #pragma vector always 2023-03-30T02:21:52,259 | 2023-03-30T02:21:52,263 MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: 2023-03-30T02:21:52,264 MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] 2023-03-30T02:21:52,264 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { 2023-03-30T02:21:52,264 | ^~ 2023-03-30T02:21:52,264 In file included from /usr/include/python3.9/Python.h:97, 2023-03-30T02:21:52,265 from MDAnalysis/lib/src/transformations/transformations.c:68: 2023-03-30T02:21:52,265 /usr/include/python3.9/unicodeobject.h:177:43: note: declared here 2023-03-30T02:21:52,265 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( 2023-03-30T02:21:52,265 | ^~~~~~~~~~~~~~~~~ 2023-03-30T02:21:52,300 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: 2023-03-30T02:21:52,301 MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,301 3427 | #pragma vector always 2023-03-30T02:21:52,301 | 2023-03-30T02:21:52,303 MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,304 3508 | #pragma vector always 2023-03-30T02:21:52,304 | 2023-03-30T02:21:52,309 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: 2023-03-30T02:21:52,309 MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,309 3610 | #pragma vector always 2023-03-30T02:21:52,309 | 2023-03-30T02:21:52,309 MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,310 3615 | #pragma vector always 2023-03-30T02:21:52,310 | 2023-03-30T02:21:52,313 MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,313 3679 | #pragma vector always 2023-03-30T02:21:52,313 | 2023-03-30T02:21:52,314 MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-03-30T02:21:52,314 3684 | #pragma vector always 2023-03-30T02:21:52,314 | 2023-03-30T02:21:52,384 At top level: 2023-03-30T02:21:52,384 MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] 2023-03-30T02:21:52,384 910 | PyConverter_DoubleVector4Copy( 2023-03-30T02:21:52,384 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:21:52,385 MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] 2023-03-30T02:21:52,385 804 | PyConverter_DoubleArrayOrNone( 2023-03-30T02:21:52,385 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:21:52,385 MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] 2023-03-30T02:21:52,385 774 | PyConverter_DoubleArray( 2023-03-30T02:21:52,385 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:21:58,181 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 2023-03-30T02:21:58,319 building 'MDAnalysis.lib.formats.libmdaxdr' extension 2023-03-30T02:21:58,320 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-03-30T02:21:58,322 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-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats -I/tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:21:58,355 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:21:58,663 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:21:58,663 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:21:58,663 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:21:58,664 from MDAnalysis/lib/formats/libmdaxdr.c:802: 2023-03-30T02:21:58,664 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:21:58,664 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:21:58,664 | ^~~~~~~ 2023-03-30T02:21:58,700 In file included from MDAnalysis/lib/formats/libmdaxdr.c:811: 2023-03-30T02:21:58,701 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:21:58,701 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:21:58,701 | 2023-03-30T02:21:58,702 In file included from MDAnalysis/lib/formats/libmdaxdr.c:812: 2023-03-30T02:21:58,702 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:21:58,702 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:21:58,702 | 2023-03-30T02:21:58,703 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-03-30T02:21:58,703 from MDAnalysis/lib/formats/libmdaxdr.c:812: 2023-03-30T02:21:58,703 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:21:58,703 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:21:58,703 | 2023-03-30T02:21:58,703 In file included from MDAnalysis/lib/formats/libmdaxdr.c:813: 2023-03-30T02:21:58,704 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:21:58,704 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:21:58,704 | 2023-03-30T02:22:30,864 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-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats -I/tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:22:30,894 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:22:30,947 In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: 2023-03-30T02:22:30,948 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:30,948 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:30,948 | 2023-03-30T02:22:30,953 In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: 2023-03-30T02:22:30,953 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:30,953 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:30,953 | 2023-03-30T02:22:30,953 In file included from /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2023-03-30T02:22:30,954 from MDAnalysis/lib/formats/src/trr_seek.c:31: 2023-03-30T02:22:30,954 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:30,954 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:30,954 | 2023-03-30T02:22:30,956 MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’: 2023-03-30T02:22:30,957 MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable] 2023-03-30T02:22:30,957 39 | int result, framebytes, totalframebytes; 2023-03-30T02:22:30,957 | ^~~~~~~~~~~~~~~ 2023-03-30T02:22:30,957 MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable] 2023-03-30T02:22:30,958 38 | float time, lambda; 2023-03-30T02:22:30,958 | ^~~~~~ 2023-03-30T02:22:30,958 MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable] 2023-03-30T02:22:30,958 38 | float time, lambda; 2023-03-30T02:22:30,958 | ^~~~ 2023-03-30T02:22:31,065 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-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats -I/tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:22:31,093 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:22:31,190 In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: 2023-03-30T02:22:31,190 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:31,191 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:31,191 | 2023-03-30T02:22:31,200 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’: 2023-03-30T02:22:31,200 MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-03-30T02:22:31,200 501 | while (size >= num && num_of_bits < 32) 2023-03-30T02:22:31,200 | ^~ 2023-03-30T02:22:31,200 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’: 2023-03-30T02:22:31,201 MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:22:31,201 547 | while (bytes[num_of_bytes] >= num) 2023-03-30T02:22:31,201 | ^~ 2023-03-30T02:22:31,201 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’: 2023-03-30T02:22:31,202 MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-03-30T02:22:31,202 656 | if (num_of_bits >= num_of_bytes * 8) 2023-03-30T02:22:31,202 | ^~ 2023-03-30T02:22:31,202 MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-03-30T02:22:31,202 658 | for (i = 0; i < num_of_bytes; i++) 2023-03-30T02:22:31,202 | ^ 2023-03-30T02:22:31,203 MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-03-30T02:22:31,203 666 | for (i = 0; i < num_of_bytes-1; i++) 2023-03-30T02:22:31,203 | ^ 2023-03-30T02:22:31,203 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’: 2023-03-30T02:22:31,203 MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:22:31,203 706 | if (lastbits < num_of_bits) 2023-03-30T02:22:31,203 | ^ 2023-03-30T02:22:31,204 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-03-30T02:22:31,205 MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:22:31,205 816 | if(size3>xfp->buf1size) 2023-03-30T02:22:31,205 | ^ 2023-03-30T02:22:31,206 MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:22:31,206 868 | maxidx = (LASTIDXxfp->buf1size) 2023-03-30T02:22:31,211 | ^ 2023-03-30T02:22:31,214 MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-03-30T02:22:31,215 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2023-03-30T02:22:31,215 | ^ 2023-03-30T02:22:31,215 MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:22:31,215 1141 | maxidx = (LASTIDXxfp->buf1size) 2023-03-30T02:22:31,221 | ^ 2023-03-30T02:22:31,222 MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:22:31,222 1368 | maxidx = (LASTIDXxfp->buf1size) { 2023-03-30T02:22:31,228 | ^ 2023-03-30T02:22:31,234 MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-03-30T02:22:31,234 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2023-03-30T02:22:31,234 | ^ 2023-03-30T02:22:31,234 MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-03-30T02:22:31,234 1624 | maxidx = (LASTIDX maxsize) 2023-03-30T02:22:32,895 | ^ 2023-03-30T02:22:32,896 MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here 2023-03-30T02:22:32,896 2335 | unsigned int size; 2023-03-30T02:22:32,897 | ^~~~ 2023-03-30T02:22:33,332 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-03-30T02:22:33,332 MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-03-30T02:22:33,332 1157 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2023-03-30T02:22:33,333 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-03-30T02:22:33,333 MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-03-30T02:22:33,333 1156 | abs(thiscoord[1] - prevcoord[1]) < larger && 2023-03-30T02:22:33,333 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-03-30T02:22:33,333 MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-03-30T02:22:33,334 1155 | abs(thiscoord[0] - prevcoord[0]) < larger && 2023-03-30T02:22:33,334 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-03-30T02:22:34,086 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-03-30T02:22:34,087 MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-03-30T02:22:34,087 1639 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2023-03-30T02:22:34,087 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-03-30T02:22:34,087 MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-03-30T02:22:34,087 1638 | abs(thiscoord[1] - prevcoord[1]) < larger && 2023-03-30T02:22:34,088 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-03-30T02:22:34,088 MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-03-30T02:22:34,088 1637 | abs(thiscoord[0] - prevcoord[0]) < larger && 2023-03-30T02:22:34,089 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-03-30T02:22:35,123 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-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats -I/tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:22:35,150 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:22:35,202 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: 2023-03-30T02:22:35,202 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:35,202 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:35,203 | 2023-03-30T02:22:35,207 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2023-03-30T02:22:35,207 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:35,207 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:35,207 | 2023-03-30T02:22:35,208 In file included from /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2023-03-30T02:22:35,208 from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2023-03-30T02:22:35,208 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:35,208 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:35,208 | 2023-03-30T02:22:35,209 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’: 2023-03-30T02:22:35,209 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] 2023-03-30T02:22:35,210 78 | if (slen != strlen(version) + 1) 2023-03-30T02:22:35,210 | ^~ 2023-03-30T02:22:35,210 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] 2023-03-30T02:22:35,210 86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) 2023-03-30T02:22:35,210 | ^~ 2023-03-30T02:22:35,225 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’: 2023-03-30T02:22:35,225 MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized] 2023-03-30T02:22:35,226 408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); 2023-03-30T02:22:35,226 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:22:36,325 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-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats -I/tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:22:36,353 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:22:36,377 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: 2023-03-30T02:22:36,377 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:36,378 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:36,378 | 2023-03-30T02:22:36,390 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2023-03-30T02:22:36,390 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:36,390 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:36,390 | 2023-03-30T02:22:36,391 In file included from /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-03-30T02:22:36,391 from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2023-03-30T02:22:36,391 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:36,391 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:36,391 | 2023-03-30T02:22:36,520 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats -I/tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:22:36,547 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:22:36,572 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: 2023-03-30T02:22:36,572 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:36,572 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:36,572 | 2023-03-30T02:22:36,584 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2023-03-30T02:22:36,585 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:36,585 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:36,585 | 2023-03-30T02:22:36,586 In file included from /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-03-30T02:22:36,586 from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2023-03-30T02:22:36,586 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-03-30T02:22:36,586 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-03-30T02:22:36,586 | 2023-03-30T02:22:36,750 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 2023-03-30T02:22:36,989 building 'MDAnalysis.lib.formats.cython_util' extension 2023-03-30T02:22:36,990 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-0gfbkp6c/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 2023-03-30T02:22:37,025 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:22:37,336 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:22:37,336 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:22:37,336 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:22:37,336 from MDAnalysis/lib/formats/cython_util.c:775: 2023-03-30T02:22:37,337 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:22:37,337 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:22:37,337 | ^~~~~~~ 2023-03-30T02:22:54,142 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 2023-03-30T02:22:54,309 building 'MDAnalysis.analysis.encore.cutils' extension 2023-03-30T02:22:54,310 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-03-30T02:22:54,310 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-03-30T02:22:54,312 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-0gfbkp6c/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 2023-03-30T02:22:54,341 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:22:54,655 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:22:54,655 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:22:54,655 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:22:54,656 from MDAnalysis/analysis/encore/cutils.c:775: 2023-03-30T02:22:54,656 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:22:54,656 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:22:54,656 | ^~~~~~~ 2023-03-30T02:22:57,278 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 2023-03-30T02:22:57,394 building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension 2023-03-30T02:22:57,395 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-03-30T02:22:57,397 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-03-30T02:22:57,398 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-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:22:57,427 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:22:57,761 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:22:57,761 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:22:57,762 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:22:57,762 from MDAnalysis/analysis/encore/clustering/affinityprop.c:781: 2023-03-30T02:22:57,762 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:22:57,762 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:22:57,762 | ^~~~~~~ 2023-03-30T02:23:08,268 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-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:23:08,293 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:23:09,317 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 2023-03-30T02:23:09,457 building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension 2023-03-30T02:23:09,459 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:23:09,460 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-03-30T02:23:09,461 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-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:23:09,492 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:23:10,178 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-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:23:10,202 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:23:10,515 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:23:10,516 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:23:10,516 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:23:10,516 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:781: 2023-03-30T02:23:10,516 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:23:10,516 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:23:10,516 | ^~~~~~~ 2023-03-30T02:23:14,977 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 2023-03-30T02:23:15,110 building 'MDAnalysis.lib._cutil' extension 2023-03-30T02:23:15,111 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-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:23:15,167 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:23:15,456 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:23:15,456 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:23:15,456 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:23:15,456 from MDAnalysis/lib/_cutil.cpp:795: 2023-03-30T02:23:15,457 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:23:15,457 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:23:15,457 | ^~~~~~~ 2023-03-30T02:23:18,359 In file included from MDAnalysis/lib/_cutil.cpp:824: 2023-03-30T02:23:18,359 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,359 827 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,359 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,359 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,360 791 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,360 | ^~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,360 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,360 764 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,360 | ^~~~~~~~~~~~~~ 2023-03-30T02:23:18,361 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,361 689 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,361 | ^~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,361 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,361 647 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,361 | ^~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,362 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,362 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,362 | ^~~~~~~~~~~ 2023-03-30T02:23:18,362 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,362 596 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,363 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,363 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,363 573 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,363 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,363 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,363 557 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2023-03-30T02:23:18,363 | ^~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,363 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,364 505 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-03-30T02:23:18,364 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,364 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,364 472 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2023-03-30T02:23:18,364 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,364 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,364 448 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2023-03-30T02:23:18,365 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,365 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,365 424 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-03-30T02:23:18,365 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,365 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,365 399 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2023-03-30T02:23:18,365 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,366 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:23:18,366 381 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2023-03-30T02:23:18,366 | ^~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:23:18,366 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/MDAnalysis/lib/include/calc_distances.h:116:13: warning: ‘void _ortho_pbc(float (*)[3], uint64_t, float*)’ defined but not used [-Wunused-function] 2023-03-30T02:23:18,366 116 | static void _ortho_pbc(coordinate* coords, uint64_t numcoords, float* box) 2023-03-30T02:23:18,366 | ^~~~~~~~~~ 2023-03-30T02:23:44,904 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 2023-03-30T02:23:45,278 building 'MDAnalysis.lib._augment' extension 2023-03-30T02:23:45,278 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-0gfbkp6c/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 2023-03-30T02:23:45,312 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:23:45,547 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:23:45,547 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:23:45,548 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:23:45,548 from MDAnalysis/lib/_augment.cpp:790: 2023-03-30T02:23:45,548 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:23:45,548 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:23:45,548 | ^~~~~~~ 2023-03-30T02:24:11,217 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 2023-03-30T02:24:11,553 building 'MDAnalysis.lib.nsgrid' extension 2023-03-30T02:24:11,555 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-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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 2023-03-30T02:24:11,589 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:24:14,042 In file included from MDAnalysis/lib/nsgrid.cpp:791: 2023-03-30T02:24:14,042 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,042 827 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,042 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,043 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,043 791 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,043 | ^~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,043 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,043 764 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,044 | ^~~~~~~~~~~~~~ 2023-03-30T02:24:14,044 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,044 689 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,044 | ^~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,044 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,045 647 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,045 | ^~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,045 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,045 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,045 | ^~~~~~~~~~~ 2023-03-30T02:24:14,045 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,045 596 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,046 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,046 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,046 573 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,046 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,046 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,046 557 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2023-03-30T02:24:14,046 | ^~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,047 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,047 505 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-03-30T02:24:14,047 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,047 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,047 472 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2023-03-30T02:24:14,047 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,047 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,048 448 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2023-03-30T02:24:14,048 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,048 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,048 424 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-03-30T02:24:14,048 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,048 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,049 399 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2023-03-30T02:24:14,049 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:14,049 /tmp/pip-wheel-rkwft2xe/mdanalysis_f2092598d93f42bd834dfdfd73538f8d/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] 2023-03-30T02:24:14,049 381 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2023-03-30T02:24:14,049 | ^~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:36,712 In file included from /usr/include/c++/10/vector:72, 2023-03-30T02:24:36,712 from MDAnalysis/lib/nsgrid.cpp:789: 2023-03-30T02:24:36,713 /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]’: 2023-03-30T02:24:36,713 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-03-30T02:24:36,713 426 | vector<_Tp, _Alloc>:: 2023-03-30T02:24:36,713 | ^~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:36,749 In file included from /usr/include/c++/10/vector:67, 2023-03-30T02:24:36,749 from MDAnalysis/lib/nsgrid.cpp:789: 2023-03-30T02:24:36,749 /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)’: 2023-03-30T02:24:36,749 /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 2023-03-30T02:24:36,750 1198 | _M_realloc_insert(end(), __x); 2023-03-30T02:24:36,750 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-03-30T02:24:36,786 In file included from /usr/include/c++/10/vector:72, 2023-03-30T02:24:36,787 from MDAnalysis/lib/nsgrid.cpp:789: 2023-03-30T02:24:36,787 /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]’: 2023-03-30T02:24:36,787 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-03-30T02:24:36,787 426 | vector<_Tp, _Alloc>:: 2023-03-30T02:24:36,787 | ^~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:37,037 /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*)’: 2023-03-30T02:24:37,038 /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 2023-03-30T02:24:37,038 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-03-30T02:24:37,038 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-03-30T02:24:40,393 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 2023-03-30T02:24:40,758 building 'MDAnalysis.coordinates.timestep' extension 2023-03-30T02:24:40,760 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-03-30T02:24:40,761 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-0gfbkp6c/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 2023-03-30T02:24:40,794 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-03-30T02:24:41,025 In file included from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-03-30T02:24:41,026 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-03-30T02:24:41,026 from /tmp/pip-build-env-0gfbkp6c/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-03-30T02:24:41,026 from MDAnalysis/coordinates/timestep.cpp:791: 2023-03-30T02:24:41,026 /tmp/pip-build-env-0gfbkp6c/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] 2023-03-30T02:24:41,026 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-03-30T02:24:41,026 | ^~~~~~~ 2023-03-30T02:24:59,005 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 2023-03-30T02:24:59,240 installing to build/bdist.linux-armv7l/wheel 2023-03-30T02:24:59,240 running install 2023-03-30T02:24:59,267 running install_lib 2023-03-30T02:24:59,276 creating build/bdist.linux-armv7l 2023-03-30T02:24:59,277 creating build/bdist.linux-armv7l/wheel 2023-03-30T02:24:59,279 creating build/bdist.linux-armv7l/wheel/MDAnalysis 2023-03-30T02:24:59,281 creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-03-30T02:24:59,283 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-03-30T02:24:59,285 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-03-30T02:24:59,288 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-03-30T02:24:59,291 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-03-30T02:24:59,294 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-03-30T02:24:59,296 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-03-30T02:24:59,299 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-03-30T02:24:59,302 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-03-30T02:24:59,304 creating build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,306 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,311 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,317 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,320 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,323 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,326 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,331 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,335 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,340 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/accessors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-03-30T02:24:59,343 creating build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-03-30T02:24:59,344 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-03-30T02:24:59,348 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-03-30T02:24:59,351 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-03-30T02:24:59,354 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-03-30T02:24:59,357 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-03-30T02:24:59,361 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-03-30T02:24:59,364 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-03-30T02:24:59,368 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,369 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,419 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,422 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,426 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,432 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,476 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,480 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,489 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,492 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,494 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,521 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 2023-03-30T02:24:59,530 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,535 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,538 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,550 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src 2023-03-30T02:24:59,552 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-03-30T02:24:59,553 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-03-30T02:24:59,556 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-03-30T02:24:59,561 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-03-30T02:24:59,563 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/correlations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,566 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,576 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,601 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,603 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,606 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,624 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,659 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,660 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 2023-03-30T02:24:59,701 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,704 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,706 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,735 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,762 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-03-30T02:24:59,763 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-03-30T02:24:59,765 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-03-30T02:24:59,767 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-03-30T02:24:59,772 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-03-30T02:24:59,774 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-03-30T02:24:59,776 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 2023-03-30T02:24:59,824 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,854 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,856 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,858 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,861 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 2023-03-30T02:24:59,883 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,886 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-03-30T02:24:59,889 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,890 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,892 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,895 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,897 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,899 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,901 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,904 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,906 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-03-30T02:24:59,909 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,912 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,941 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,980 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis 2023-03-30T02:24:59,981 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis 2023-03-30T02:24:59,983 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,986 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,989 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,992 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:24:59,996 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:25:00,000 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-03-30T02:25:00,018 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include 2023-03-30T02:25:00,019 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include 2023-03-30T02:25:00,023 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-03-30T02:25:00,026 creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-03-30T02:25:00,027 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-03-30T02:25:00,030 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-03-30T02:25:00,032 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-03-30T02:25:00,036 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,037 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,040 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,043 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-03-30T02:25:00,044 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-03-30T02:25:00,047 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-03-30T02:25:00,050 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-03-30T02:25:00,052 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-03-30T02:25:00,055 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,058 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,061 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,063 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,065 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,068 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,070 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,072 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,075 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,077 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,080 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,083 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,086 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,089 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,091 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,094 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,096 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,100 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,102 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,105 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,107 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,109 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,113 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,115 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,117 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,120 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-03-30T02:25:00,123 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-03-30T02:25:00,125 creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,127 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,129 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,132 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,135 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,137 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,140 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,143 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,146 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/wrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-03-30T02:25:00,149 creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-03-30T02:25:00,150 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-03-30T02:25:00,152 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-03-30T02:25:00,155 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-03-30T02:25:00,158 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-03-30T02:25:00,162 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-03-30T02:25:00,165 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-03-30T02:25:00,168 creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-03-30T02:25:00,169 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-03-30T02:25:00,171 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-03-30T02:25:00,174 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,175 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,181 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,184 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-03-30T02:25:00,185 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-03-30T02:25:00,189 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-03-30T02:25:00,191 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-03-30T02:25:00,194 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-03-30T02:25:00,199 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/msd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,202 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,204 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,208 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,211 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,214 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,217 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/bat.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,220 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,225 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:25:00,226 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:25:00,230 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:25:00,232 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:25:00,235 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-03-30T02:25:00,239 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,242 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,245 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,247 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,250 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,252 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,256 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-03-30T02:25:00,257 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-03-30T02:25:00,260 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-03-30T02:25:00,262 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-03-30T02:25:00,264 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-03-30T02:25:00,268 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,272 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,274 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,278 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,282 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,285 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-03-30T02:25:00,286 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-03-30T02:25:00,289 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-03-30T02:25:00,291 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,294 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,295 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,302 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,306 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,309 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,311 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,313 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,315 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,318 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 2023-03-30T02:25:00,324 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-03-30T02:25:00,327 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:25:00,328 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:25:00,330 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:25:00,333 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-03-30T02:25:00,334 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 2023-03-30T02:25:00,337 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 2023-03-30T02:25:00,340 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:25:00,342 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-03-30T02:25:00,352 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 2023-03-30T02:25:00,365 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-03-30T02:25:00,366 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 2023-03-30T02:25:00,369 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-03-30T02:25:00,370 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 2023-03-30T02:25:00,389 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src 2023-03-30T02:25:00,390 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src 2023-03-30T02:25:00,393 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-03-30T02:25:00,395 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-03-30T02:25:00,397 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-03-30T02:25:00,407 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-03-30T02:25:00,410 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-03-30T02:25:00,414 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include 2023-03-30T02:25:00,415 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include 2023-03-30T02:25:00,417 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-03-30T02:25:00,420 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-03-30T02:25:00,423 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-03-30T02:25:00,424 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-03-30T02:25:00,426 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-03-30T02:25:00,429 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-03-30T02:25:00,432 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,433 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,435 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,438 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,440 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,443 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,445 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,448 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,450 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,453 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,455 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,458 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,483 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,485 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,488 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,491 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,494 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,496 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,500 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,503 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,508 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,513 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,518 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,522 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,525 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,529 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,555 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,557 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,561 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,563 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,565 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,568 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,572 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,574 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,577 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,580 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,582 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,585 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-03-30T02:25:00,588 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-03-30T02:25:00,590 running install_egg_info 2023-03-30T02:25:00,597 Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-2.4.3-py3.9.egg-info 2023-03-30T02:25:00,614 running install_scripts 2023-03-30T02:25:00,684 creating build/bdist.linux-armv7l/wheel/MDAnalysis-2.4.3.dist-info/WHEEL 2023-03-30T02:25:00,688 creating '/tmp/pip-wheel-s0rqv8fr/.tmp-l6wwrgst/MDAnalysis-2.4.3-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-03-30T02:25:00,691 adding 'MDAnalysis/__init__.py' 2023-03-30T02:25:00,693 adding 'MDAnalysis/authors.py' 2023-03-30T02:25:00,694 adding 'MDAnalysis/due.py' 2023-03-30T02:25:00,696 adding 'MDAnalysis/exceptions.py' 2023-03-30T02:25:00,698 adding 'MDAnalysis/units.py' 2023-03-30T02:25:00,700 adding 'MDAnalysis/version.py' 2023-03-30T02:25:00,703 adding 'MDAnalysis/analysis/__init__.py' 2023-03-30T02:25:00,711 adding 'MDAnalysis/analysis/align.py' 2023-03-30T02:25:00,714 adding 'MDAnalysis/analysis/base.py' 2023-03-30T02:25:00,718 adding 'MDAnalysis/analysis/bat.py' 2023-03-30T02:25:00,721 adding 'MDAnalysis/analysis/contacts.py' 2023-03-30T02:25:00,726 adding 'MDAnalysis/analysis/density.py' 2023-03-30T02:25:00,728 adding 'MDAnalysis/analysis/dielectric.py' 2023-03-30T02:25:00,731 adding 'MDAnalysis/analysis/diffusionmap.py' 2023-03-30T02:25:00,734 adding 'MDAnalysis/analysis/dihedrals.py' 2023-03-30T02:25:00,736 adding 'MDAnalysis/analysis/distances.py' 2023-03-30T02:25:00,739 adding 'MDAnalysis/analysis/gnm.py' 2023-03-30T02:25:00,742 adding 'MDAnalysis/analysis/helix_analysis.py' 2023-03-30T02:25:00,744 adding 'MDAnalysis/analysis/leaflet.py' 2023-03-30T02:25:00,747 adding 'MDAnalysis/analysis/lineardensity.py' 2023-03-30T02:25:00,750 adding 'MDAnalysis/analysis/msd.py' 2023-03-30T02:25:00,752 adding 'MDAnalysis/analysis/nucleicacids.py' 2023-03-30T02:25:00,754 adding 'MDAnalysis/analysis/nuclinfo.py' 2023-03-30T02:25:00,759 adding 'MDAnalysis/analysis/pca.py' 2023-03-30T02:25:00,761 adding 'MDAnalysis/analysis/polymer.py' 2023-03-30T02:25:00,771 adding 'MDAnalysis/analysis/psa.py' 2023-03-30T02:25:00,774 adding 'MDAnalysis/analysis/rdf.py' 2023-03-30T02:25:00,779 adding 'MDAnalysis/analysis/rms.py' 2023-03-30T02:25:00,784 adding 'MDAnalysis/analysis/waterdynamics.py' 2023-03-30T02:25:00,786 adding 'MDAnalysis/analysis/data/__init__.py' 2023-03-30T02:25:00,788 adding 'MDAnalysis/analysis/data/filenames.py' 2023-03-30T02:25:00,792 adding 'MDAnalysis/analysis/data/janin_ref_data.npy' 2023-03-30T02:25:00,797 adding 'MDAnalysis/analysis/data/rama_ref_data.npy' 2023-03-30T02:25:00,800 adding 'MDAnalysis/analysis/encore/__init__.py' 2023-03-30T02:25:00,802 adding 'MDAnalysis/analysis/encore/bootstrap.py' 2023-03-30T02:25:00,804 adding 'MDAnalysis/analysis/encore/confdistmatrix.py' 2023-03-30T02:25:00,806 adding 'MDAnalysis/analysis/encore/covariance.py' 2023-03-30T02:25:00,828 adding 'MDAnalysis/analysis/encore/cutils.c' 2023-03-30T02:25:00,865 adding 'MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:00,867 adding 'MDAnalysis/analysis/encore/cutils.pyx' 2023-03-30T02:25:00,874 adding 'MDAnalysis/analysis/encore/similarity.py' 2023-03-30T02:25:00,877 adding 'MDAnalysis/analysis/encore/utils.py' 2023-03-30T02:25:00,879 adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' 2023-03-30T02:25:00,882 adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' 2023-03-30T02:25:00,884 adding 'MDAnalysis/analysis/encore/clustering/__init__.py' 2023-03-30T02:25:00,914 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' 2023-03-30T02:25:01,022 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:01,026 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' 2023-03-30T02:25:01,028 adding 'MDAnalysis/analysis/encore/clustering/cluster.py' 2023-03-30T02:25:01,030 adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' 2023-03-30T02:25:01,033 adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' 2023-03-30T02:25:01,035 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' 2023-03-30T02:25:01,037 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' 2023-03-30T02:25:01,039 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' 2023-03-30T02:25:01,062 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' 2023-03-30T02:25:01,130 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:01,134 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' 2023-03-30T02:25:01,136 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' 2023-03-30T02:25:01,138 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' 2023-03-30T02:25:01,140 adding 'MDAnalysis/analysis/hbonds/__init__.py' 2023-03-30T02:25:01,141 adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' 2023-03-30T02:25:01,144 adding 'MDAnalysis/analysis/hole2/__init__.py' 2023-03-30T02:25:01,150 adding 'MDAnalysis/analysis/hole2/hole.py' 2023-03-30T02:25:01,152 adding 'MDAnalysis/analysis/hole2/templates.py' 2023-03-30T02:25:01,155 adding 'MDAnalysis/analysis/hole2/utils.py' 2023-03-30T02:25:01,157 adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' 2023-03-30T02:25:01,162 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' 2023-03-30T02:25:01,165 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' 2023-03-30T02:25:01,175 adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' 2023-03-30T02:25:01,177 adding 'MDAnalysis/analysis/legacy/__init__.py' 2023-03-30T02:25:01,181 adding 'MDAnalysis/analysis/legacy/x3dna.py' 2023-03-30T02:25:01,185 adding 'MDAnalysis/auxiliary/EDR.py' 2023-03-30T02:25:01,187 adding 'MDAnalysis/auxiliary/XVG.py' 2023-03-30T02:25:01,190 adding 'MDAnalysis/auxiliary/__init__.py' 2023-03-30T02:25:01,196 adding 'MDAnalysis/auxiliary/base.py' 2023-03-30T02:25:01,198 adding 'MDAnalysis/auxiliary/core.py' 2023-03-30T02:25:01,200 adding 'MDAnalysis/converters/OpenMM.py' 2023-03-30T02:25:01,202 adding 'MDAnalysis/converters/OpenMMParser.py' 2023-03-30T02:25:01,204 adding 'MDAnalysis/converters/ParmEd.py' 2023-03-30T02:25:01,206 adding 'MDAnalysis/converters/ParmEdParser.py' 2023-03-30T02:25:01,212 adding 'MDAnalysis/converters/RDKit.py' 2023-03-30T02:25:01,214 adding 'MDAnalysis/converters/RDKitParser.py' 2023-03-30T02:25:01,215 adding 'MDAnalysis/converters/__init__.py' 2023-03-30T02:25:01,218 adding 'MDAnalysis/coordinates/CRD.py' 2023-03-30T02:25:01,221 adding 'MDAnalysis/coordinates/DCD.py' 2023-03-30T02:25:01,223 adding 'MDAnalysis/coordinates/DLPoly.py' 2023-03-30T02:25:01,225 adding 'MDAnalysis/coordinates/DMS.py' 2023-03-30T02:25:01,227 adding 'MDAnalysis/coordinates/FHIAIMS.py' 2023-03-30T02:25:01,229 adding 'MDAnalysis/coordinates/GMS.py' 2023-03-30T02:25:01,232 adding 'MDAnalysis/coordinates/GRO.py' 2023-03-30T02:25:01,234 adding 'MDAnalysis/coordinates/GSD.py' 2023-03-30T02:25:01,241 adding 'MDAnalysis/coordinates/H5MD.py' 2023-03-30T02:25:01,243 adding 'MDAnalysis/coordinates/INPCRD.py' 2023-03-30T02:25:01,247 adding 'MDAnalysis/coordinates/LAMMPS.py' 2023-03-30T02:25:01,248 adding 'MDAnalysis/coordinates/MMTF.py' 2023-03-30T02:25:01,251 adding 'MDAnalysis/coordinates/MOL2.py' 2023-03-30T02:25:01,252 adding 'MDAnalysis/coordinates/NAMDBIN.py' 2023-03-30T02:25:01,259 adding 'MDAnalysis/coordinates/PDB.py' 2023-03-30T02:25:01,262 adding 'MDAnalysis/coordinates/PDBQT.py' 2023-03-30T02:25:01,265 adding 'MDAnalysis/coordinates/PQR.py' 2023-03-30T02:25:01,266 adding 'MDAnalysis/coordinates/ParmEd.py' 2023-03-30T02:25:01,269 adding 'MDAnalysis/coordinates/TNG.py' 2023-03-30T02:25:01,275 adding 'MDAnalysis/coordinates/TRJ.py' 2023-03-30T02:25:01,277 adding 'MDAnalysis/coordinates/TRR.py' 2023-03-30T02:25:01,280 adding 'MDAnalysis/coordinates/TRZ.py' 2023-03-30T02:25:01,282 adding 'MDAnalysis/coordinates/TXYZ.py' 2023-03-30T02:25:01,284 adding 'MDAnalysis/coordinates/XDR.py' 2023-03-30T02:25:01,286 adding 'MDAnalysis/coordinates/XTC.py' 2023-03-30T02:25:01,288 adding 'MDAnalysis/coordinates/XYZ.py' 2023-03-30T02:25:01,293 adding 'MDAnalysis/coordinates/__init__.py' 2023-03-30T02:25:01,301 adding 'MDAnalysis/coordinates/base.py' 2023-03-30T02:25:01,305 adding 'MDAnalysis/coordinates/chain.py' 2023-03-30T02:25:01,308 adding 'MDAnalysis/coordinates/chemfiles.py' 2023-03-30T02:25:01,310 adding 'MDAnalysis/coordinates/core.py' 2023-03-30T02:25:01,313 adding 'MDAnalysis/coordinates/memory.py' 2023-03-30T02:25:01,315 adding 'MDAnalysis/coordinates/null.py' 2023-03-30T02:25:01,373 adding 'MDAnalysis/coordinates/timestep.cpp' 2023-03-30T02:25:01,605 adding 'MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:01,614 adding 'MDAnalysis/coordinates/timestep.pxd' 2023-03-30T02:25:01,617 adding 'MDAnalysis/coordinates/timestep.pyx' 2023-03-30T02:25:01,620 adding 'MDAnalysis/core/__init__.py' 2023-03-30T02:25:01,622 adding 'MDAnalysis/core/_get_readers.py' 2023-03-30T02:25:01,624 adding 'MDAnalysis/core/accessors.py' 2023-03-30T02:25:01,644 adding 'MDAnalysis/core/groups.py' 2023-03-30T02:25:01,652 adding 'MDAnalysis/core/selection.py' 2023-03-30T02:25:01,655 adding 'MDAnalysis/core/topology.py' 2023-03-30T02:25:01,665 adding 'MDAnalysis/core/topologyattrs.py' 2023-03-30T02:25:01,670 adding 'MDAnalysis/core/topologyobjects.py' 2023-03-30T02:25:01,677 adding 'MDAnalysis/core/universe.py' 2023-03-30T02:25:01,681 adding 'MDAnalysis/lib/NeighborSearch.py' 2023-03-30T02:25:01,682 adding 'MDAnalysis/lib/__init__.py' 2023-03-30T02:25:01,760 adding 'MDAnalysis/lib/_augment.cpp' 2023-03-30T02:25:02,038 adding 'MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:02,048 adding 'MDAnalysis/lib/_augment.pyx' 2023-03-30T02:25:02,130 adding 'MDAnalysis/lib/_cutil.cpp' 2023-03-30T02:25:02,481 adding 'MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:02,494 adding 'MDAnalysis/lib/_cutil.pxd' 2023-03-30T02:25:02,497 adding 'MDAnalysis/lib/_cutil.pyx' 2023-03-30T02:25:02,551 adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:02,645 adding 'MDAnalysis/lib/c_distances.c' 2023-03-30T02:25:02,978 adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:02,991 adding 'MDAnalysis/lib/c_distances.pyx' 2023-03-30T02:25:03,016 adding 'MDAnalysis/lib/c_distances_openmp.c' 2023-03-30T02:25:03,081 adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:03,084 adding 'MDAnalysis/lib/c_distances_openmp.pyx' 2023-03-30T02:25:03,086 adding 'MDAnalysis/lib/correlations.py' 2023-03-30T02:25:03,093 adding 'MDAnalysis/lib/distances.py' 2023-03-30T02:25:03,095 adding 'MDAnalysis/lib/log.py' 2023-03-30T02:25:03,098 adding 'MDAnalysis/lib/mdamath.py' 2023-03-30T02:25:03,183 adding 'MDAnalysis/lib/nsgrid.cpp' 2023-03-30T02:25:03,518 adding 'MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:03,532 adding 'MDAnalysis/lib/nsgrid.pyx' 2023-03-30T02:25:03,534 adding 'MDAnalysis/lib/picklable_file_io.py' 2023-03-30T02:25:03,536 adding 'MDAnalysis/lib/pkdtree.py' 2023-03-30T02:25:03,568 adding 'MDAnalysis/lib/qcprot.c' 2023-03-30T02:25:03,645 adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:03,650 adding 'MDAnalysis/lib/qcprot.pyx' 2023-03-30T02:25:03,657 adding 'MDAnalysis/lib/transformations.py' 2023-03-30T02:25:03,669 adding 'MDAnalysis/lib/util.py' 2023-03-30T02:25:03,671 adding 'MDAnalysis/lib/formats/__init__.py' 2023-03-30T02:25:03,738 adding 'MDAnalysis/lib/formats/cython_util.c' 2023-03-30T02:25:03,948 adding 'MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:03,956 adding 'MDAnalysis/lib/formats/cython_util.pxd' 2023-03-30T02:25:03,957 adding 'MDAnalysis/lib/formats/cython_util.pyx' 2023-03-30T02:25:04,056 adding 'MDAnalysis/lib/formats/libdcd.c' 2023-03-30T02:25:04,447 adding 'MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:04,461 adding 'MDAnalysis/lib/formats/libdcd.pxd' 2023-03-30T02:25:04,464 adding 'MDAnalysis/lib/formats/libdcd.pyx' 2023-03-30T02:25:04,562 adding 'MDAnalysis/lib/formats/libmdaxdr.c' 2023-03-30T02:25:04,982 adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so' 2023-03-30T02:25:04,996 adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' 2023-03-30T02:25:05,000 adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' 2023-03-30T02:25:05,002 adding 'MDAnalysis/lib/formats/include/endianswap.h' 2023-03-30T02:25:05,004 adding 'MDAnalysis/lib/formats/include/fastio.h' 2023-03-30T02:25:05,008 adding 'MDAnalysis/lib/formats/include/readdcd.h' 2023-03-30T02:25:05,009 adding 'MDAnalysis/lib/formats/include/trr_seek.h' 2023-03-30T02:25:05,012 adding 'MDAnalysis/lib/formats/include/xdrfile.h' 2023-03-30T02:25:05,013 adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' 2023-03-30T02:25:05,015 adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' 2023-03-30T02:25:05,016 adding 'MDAnalysis/lib/formats/include/xtc_seek.h' 2023-03-30T02:25:05,018 adding 'MDAnalysis/lib/formats/src/trr_seek.c' 2023-03-30T02:25:05,025 adding 'MDAnalysis/lib/formats/src/xdrfile.c' 2023-03-30T02:25:05,027 adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' 2023-03-30T02:25:05,029 adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' 2023-03-30T02:25:05,030 adding 'MDAnalysis/lib/formats/src/xtc_seek.c' 2023-03-30T02:25:05,034 adding 'MDAnalysis/lib/include/calc_distances.h' 2023-03-30T02:25:05,036 adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' 2023-03-30T02:25:05,038 adding 'MDAnalysis/lib/src/transformations/AUTHOR' 2023-03-30T02:25:05,039 adding 'MDAnalysis/lib/src/transformations/LICENCE' 2023-03-30T02:25:05,049 adding 'MDAnalysis/lib/src/transformations/transformations.c' 2023-03-30T02:25:05,052 adding 'MDAnalysis/selections/__init__.py' 2023-03-30T02:25:05,054 adding 'MDAnalysis/selections/base.py' 2023-03-30T02:25:05,056 adding 'MDAnalysis/selections/charmm.py' 2023-03-30T02:25:05,057 adding 'MDAnalysis/selections/gromacs.py' 2023-03-30T02:25:05,058 adding 'MDAnalysis/selections/jmol.py' 2023-03-30T02:25:05,060 adding 'MDAnalysis/selections/pymol.py' 2023-03-30T02:25:05,061 adding 'MDAnalysis/selections/vmd.py' 2023-03-30T02:25:05,063 adding 'MDAnalysis/tests/__init__.py' 2023-03-30T02:25:05,065 adding 'MDAnalysis/tests/datafiles.py' 2023-03-30T02:25:05,067 adding 'MDAnalysis/topology/CRDParser.py' 2023-03-30T02:25:05,069 adding 'MDAnalysis/topology/DLPolyParser.py' 2023-03-30T02:25:05,071 adding 'MDAnalysis/topology/DMSParser.py' 2023-03-30T02:25:05,072 adding 'MDAnalysis/topology/ExtendedPDBParser.py' 2023-03-30T02:25:05,074 adding 'MDAnalysis/topology/FHIAIMSParser.py' 2023-03-30T02:25:05,075 adding 'MDAnalysis/topology/GMSParser.py' 2023-03-30T02:25:05,077 adding 'MDAnalysis/topology/GROParser.py' 2023-03-30T02:25:05,079 adding 'MDAnalysis/topology/GSDParser.py' 2023-03-30T02:25:05,080 adding 'MDAnalysis/topology/HoomdXMLParser.py' 2023-03-30T02:25:05,083 adding 'MDAnalysis/topology/ITPParser.py' 2023-03-30T02:25:05,086 adding 'MDAnalysis/topology/LAMMPSParser.py' 2023-03-30T02:25:05,088 adding 'MDAnalysis/topology/MMTFParser.py' 2023-03-30T02:25:05,090 adding 'MDAnalysis/topology/MOL2Parser.py' 2023-03-30T02:25:05,092 adding 'MDAnalysis/topology/MinimalParser.py' 2023-03-30T02:25:05,094 adding 'MDAnalysis/topology/PDBParser.py' 2023-03-30T02:25:05,096 adding 'MDAnalysis/topology/PDBQTParser.py' 2023-03-30T02:25:05,098 adding 'MDAnalysis/topology/PQRParser.py' 2023-03-30T02:25:05,100 adding 'MDAnalysis/topology/PSFParser.py' 2023-03-30T02:25:05,101 adding 'MDAnalysis/topology/ParmEdParser.py' 2023-03-30T02:25:05,105 adding 'MDAnalysis/topology/TOPParser.py' 2023-03-30T02:25:05,107 adding 'MDAnalysis/topology/TPRParser.py' 2023-03-30T02:25:05,108 adding 'MDAnalysis/topology/TXYZParser.py' 2023-03-30T02:25:05,110 adding 'MDAnalysis/topology/XYZParser.py' 2023-03-30T02:25:05,112 adding 'MDAnalysis/topology/__init__.py' 2023-03-30T02:25:05,114 adding 'MDAnalysis/topology/base.py' 2023-03-30T02:25:05,116 adding 'MDAnalysis/topology/core.py' 2023-03-30T02:25:05,118 adding 'MDAnalysis/topology/guessers.py' 2023-03-30T02:25:05,120 adding 'MDAnalysis/topology/tables.py' 2023-03-30T02:25:05,122 adding 'MDAnalysis/topology/tpr/__init__.py' 2023-03-30T02:25:05,124 adding 'MDAnalysis/topology/tpr/obj.py' 2023-03-30T02:25:05,126 adding 'MDAnalysis/topology/tpr/setting.py' 2023-03-30T02:25:05,130 adding 'MDAnalysis/topology/tpr/utils.py' 2023-03-30T02:25:05,132 adding 'MDAnalysis/transformations/__init__.py' 2023-03-30T02:25:05,134 adding 'MDAnalysis/transformations/base.py' 2023-03-30T02:25:05,135 adding 'MDAnalysis/transformations/boxdimensions.py' 2023-03-30T02:25:05,137 adding 'MDAnalysis/transformations/fit.py' 2023-03-30T02:25:05,139 adding 'MDAnalysis/transformations/positionaveraging.py' 2023-03-30T02:25:05,141 adding 'MDAnalysis/transformations/rotate.py' 2023-03-30T02:25:05,143 adding 'MDAnalysis/transformations/translate.py' 2023-03-30T02:25:05,144 adding 'MDAnalysis/transformations/wrap.py' 2023-03-30T02:25:05,146 adding 'MDAnalysis/visualization/__init__.py' 2023-03-30T02:25:05,149 adding 'MDAnalysis/visualization/streamlines.py' 2023-03-30T02:25:05,152 adding 'MDAnalysis/visualization/streamlines_3D.py' 2023-03-30T02:25:05,155 adding 'MDAnalysis-2.4.3.dist-info/AUTHORS' 2023-03-30T02:25:05,159 adding 'MDAnalysis-2.4.3.dist-info/LICENSE' 2023-03-30T02:25:05,164 adding 'MDAnalysis-2.4.3.dist-info/METADATA' 2023-03-30T02:25:05,166 adding 'MDAnalysis-2.4.3.dist-info/WHEEL' 2023-03-30T02:25:05,167 adding 'MDAnalysis-2.4.3.dist-info/top_level.txt' 2023-03-30T02:25:05,171 adding 'MDAnalysis-2.4.3.dist-info/RECORD' 2023-03-30T02:25:05,268 removing build/bdist.linux-armv7l/wheel 2023-03-30T02:25:05,552 Building wheel for mdanalysis (pyproject.toml): finished with status 'done' 2023-03-30T02:25:05,719 Created wheel for mdanalysis: filename=MDAnalysis-2.4.3-cp39-cp39-linux_armv7l.whl size=7778704 sha256=385768a1cbe3cb8f6dabd63687b4e5ed03a5bb6c39ab90c5b75914881d468334 2023-03-30T02:25:05,720 Stored in directory: /tmp/pip-ephem-wheel-cache-vuqsqqdu/wheels/0b/83/f5/3790ddfffe27ebf1e60b2831e22041d25ba111821953fd48a1 2023-03-30T02:25:05,749 Successfully built mdanalysis 2023-03-30T02:25:05,978 Removed build tracker: '/tmp/pip-build-tracker-1tslz_jx'