2022-06-02T19:36:18,755 Created temporary directory: /tmp/pip-ephem-wheel-cache-x4rsn4cl 2022-06-02T19:36:18,760 Created temporary directory: /tmp/pip-build-tracker-9e2zji9q 2022-06-02T19:36:18,761 Initialized build tracking at /tmp/pip-build-tracker-9e2zji9q 2022-06-02T19:36:18,761 Created build tracker: /tmp/pip-build-tracker-9e2zji9q 2022-06-02T19:36:18,761 Entered build tracker: /tmp/pip-build-tracker-9e2zji9q 2022-06-02T19:36:18,763 Created temporary directory: /tmp/pip-wheel-ciulgnpj 2022-06-02T19:36:18,831 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-02T19:36:18,839 2 location(s) to search for versions of mdanalysis: 2022-06-02T19:36:18,839 * https://pypi.org/simple/mdanalysis/ 2022-06-02T19:36:18,839 * https://www.piwheels.org/simple/mdanalysis/ 2022-06-02T19:36:18,840 Fetching project page and analyzing links: https://pypi.org/simple/mdanalysis/ 2022-06-02T19:36:18,841 Getting page https://pypi.org/simple/mdanalysis/ 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https://files.pythonhosted.org/packages/bc/c2/e8ba8d35609854287ec30cdb80a79e8de33f1cd88fd05efd40bdb705b142/MDAnalysis-2.2.0-cp38-cp38-win_amd64.whl#sha256=581ce428639f04a1d46a651be4c33139912714ed57c293b004de9e2fffe7d98b (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-06-02T19:36:19,025 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/17/0f/c96e22c0487dc4758d6cb895c0707c12e359b9e48d5022f7316df42f8c84/MDAnalysis-2.2.0-cp39-cp39-macosx_10_9_x86_64.whl#sha256=e1131feec575805932f36443d48375029faef60b60ba0680a86e43b3cdfa5ecb (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-06-02T19:36:19,025 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/50/d9/af23d161bc9c50678f955d802b8cb1ab624e715ed7d86e8e14f86e4b8f80/MDAnalysis-2.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl#sha256=65039b454f310055f7bc2412fd49a5d25535f81ce87a7bdb0f91dfa7872d4bf9 (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-06-02T19:36:19,026 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/83/5c/464d58a27ce0e2b0f010b1c65d0b4149256a7c470f5076beee1928e5e9a9/MDAnalysis-2.2.0-cp39-cp39-win_amd64.whl#sha256=0d067a4fee8efe602b95809c21b69de1509da15dfee9e5de714fa139ce1a9157 (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2022-06-02T19:36:19,027 Found link https://files.pythonhosted.org/packages/5b/73/a077ff42d0cd88c5d3d6320fb156811cf67b28b5ea09a3c800e31af84b9b/MDAnalysis-2.2.0.tar.gz#sha256=bf9c9b7a03404e65aad66215d4c2ff8834ab747551eeaee059ff3e599a99d322 (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8), version: 2.2.0 2022-06-02T19:36:19,028 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdanalysis/ 2022-06-02T19:36:19,028 Getting page https://www.piwheels.org/simple/mdanalysis/ 2022-06-02T19:36:19,030 Found index url https://www.piwheels.org/simple 2022-06-02T19:36:19,311 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.1.0-cp39-cp39-linux_armv7l.whl#sha256=d9556ba8add30ef268b271c12910975221cca955af752f664094b594c5290f82 (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.7) 2022-06-02T19:36:19,311 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.1.0-cp39-cp39-linux_armv6l.whl#sha256=d9556ba8add30ef268b271c12910975221cca955af752f664094b594c5290f82 (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.7) 2022-06-02T19:36:19,312 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.1.0-cp37-cp37m-linux_armv7l.whl#sha256=15211cf0c7bf4819d9c48762d3c10d7541b273818dfe16cade585528469acb6e (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.7) 2022-06-02T19:36:19,312 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.1.0-cp37-cp37m-linux_armv6l.whl#sha256=15211cf0c7bf4819d9c48762d3c10d7541b273818dfe16cade585528469acb6e (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.7) 2022-06-02T19:36:19,313 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.0.0-cp39-cp39-linux_armv7l.whl#sha256=565f74ce6e9dd72729736ca534c18c243dfa384a984c24dd759f1a263cd3c98c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.6) 2022-06-02T19:36:19,313 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.0.0-cp39-cp39-linux_armv6l.whl#sha256=565f74ce6e9dd72729736ca534c18c243dfa384a984c24dd759f1a263cd3c98c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.6) 2022-06-02T19:36:19,314 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.0.0b0-cp39-cp39-linux_armv6l.whl#sha256=6faa74b3b1a64cdd53a1313f3ecf13a260e99df077e63a45b273edd2b5afc680 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,316 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.0.0b0-cp37-cp37m-linux_armv7l.whl#sha256=331239f905d05b614d662e8a60615f80c2611d8f6ea8f3e256a0cbcefdf53191 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,316 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.0.0b0-cp37-cp37m-linux_armv6l.whl#sha256=331239f905d05b614d662e8a60615f80c2611d8f6ea8f3e256a0cbcefdf53191 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,317 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=636760cd892a8524f5912fafc58d29ffcce61acbd8730c7c69a3e922a164476f (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2022-06-02T19:36:19,318 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=636760cd892a8524f5912fafc58d29ffcce61acbd8730c7c69a3e922a164476f (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2022-06-02T19:36:19,318 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.1.0-cp37-cp37m-linux_armv7l.whl#sha256=9693d11a44eeb74415f6614dca0791bfe7f0cf24552a0ed3d17c133ff5b361ef (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2022-06-02T19:36:19,319 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.1.0-cp37-cp37m-linux_armv6l.whl#sha256=9693d11a44eeb74415f6614dca0791bfe7f0cf24552a0ed3d17c133ff5b361ef (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2022-06-02T19:36:19,319 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.1-cp37-cp37m-linux_armv7l.whl#sha256=1214ca3490e50243b48350c6c6a2c89b77cce8f1cd72f6d2549860b3db1ad84c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2022-06-02T19:36:19,319 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=1214ca3490e50243b48350c6c6a2c89b77cce8f1cd72f6d2549860b3db1ad84c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2022-06-02T19:36:19,320 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=e43dbbd4ecd06fb475d80e5dae571708415e1287e6dd2c669c98095e13ea2ae8 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,320 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/) 2022-06-02T19:36:19,321 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/) 2022-06-02T19:36:19,321 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/) 2022-06-02T19:36:19,322 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/) 2022-06-02T19:36:19,322 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp35-cp35m-linux_armv7l.whl#sha256=b669220c967a8cc746ae35c931d22da666f540595d1e9a9c3bb620effa9205b3 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,323 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp34-cp34m-linux_armv7l.whl#sha256=73adf04061df9ef3a9987e05113ccef5654aba2f3d2a3fe680ad590a76b2cd4c (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,323 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp34-cp34m-linux_armv6l.whl#sha256=73adf04061df9ef3a9987e05113ccef5654aba2f3d2a3fe680ad590a76b2cd4c (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,324 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.1-cp39-cp39-linux_armv7l.whl#sha256=89f6feff5fc44ebffd65aa746c268db44a975620306dfebc09a8e7b8e9d5e4da (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,324 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.1-cp39-cp39-linux_armv6l.whl#sha256=89f6feff5fc44ebffd65aa746c268db44a975620306dfebc09a8e7b8e9d5e4da (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,325 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.1-cp35-cp35m-linux_armv7l.whl#sha256=dafe9f34f8fc19527a5e2ebbe3080bfa1e89a5ceb160e8a52bf3ca2a9dce6442 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,325 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.1-cp35-cp35m-linux_armv6l.whl#sha256=dafe9f34f8fc19527a5e2ebbe3080bfa1e89a5ceb160e8a52bf3ca2a9dce6442 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,326 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.1-cp37-cp37m-linux_armv6l.whl#sha256=51964d1254a62b7b673ddfa8ce4eb6616d3b13f1ea26702fc5ba1ea0a2d30696 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,326 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.1-cp37-cp37m-linux_armv7l.whl#sha256=51964d1254a62b7b673ddfa8ce4eb6616d3b13f1ea26702fc5ba1ea0a2d30696 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,327 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.0-cp39-cp39-linux_armv7l.whl#sha256=71f4f4953090bbbbafab4e8e5f1af9286acd1dbe6863f95771e62ca51d6772be (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,327 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.0-cp39-cp39-linux_armv6l.whl#sha256=71f4f4953090bbbbafab4e8e5f1af9286acd1dbe6863f95771e62ca51d6772be (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,328 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.0-cp37-cp37m-linux_armv7l.whl#sha256=9b6fa10f5b5f2473db79f5704fbfc697f53d7c356f152ba8d80c761e63acbed7 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,328 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.0-cp37-cp37m-linux_armv6l.whl#sha256=9b6fa10f5b5f2473db79f5704fbfc697f53d7c356f152ba8d80c761e63acbed7 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,329 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp34-cp34m-linux_armv7l.whl#sha256=2182ab1095b6fb7758816fb8041d325e39216149dd9cc19f98b2394392a14f1b (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,335 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/) 2022-06-02T19:36:19,336 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/) 2022-06-02T19:36:19,336 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/) 2022-06-02T19:36:19,337 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/) 2022-06-02T19:36:19,337 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/) 2022-06-02T19:36:19,338 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/) 2022-06-02T19:36:19,338 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/) 2022-06-02T19:36:19,339 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/) 2022-06-02T19:36:19,339 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/) 2022-06-02T19:36:19,339 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/) 2022-06-02T19:36:19,340 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/) 2022-06-02T19:36:19,340 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/) 2022-06-02T19:36:19,341 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/) 2022-06-02T19:36:19,341 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/) 2022-06-02T19:36:19,342 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/) 2022-06-02T19:36:19,342 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/) 2022-06-02T19:36:19,343 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/) 2022-06-02T19:36:19,343 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/) 2022-06-02T19:36:19,344 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/) 2022-06-02T19:36:19,344 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/) 2022-06-02T19:36:19,345 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/) 2022-06-02T19:36:19,345 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/) 2022-06-02T19:36:19,346 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/) 2022-06-02T19:36:19,346 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/) 2022-06-02T19:36:19,347 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/) 2022-06-02T19:36:19,347 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/) 2022-06-02T19:36:19,348 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp34-cp34m-linux_armv7l.whl#sha256=34198e0f9e509df1779c2255812cee0f720dc8e989c7d4b7196337f75f1ef51b (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,348 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp35-cp35m-linux_armv7l.whl#sha256=032867bf17eecd5fd249607198ad5c191fac901f2856d5a485ffc53a8eb687d4 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,349 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/) 2022-06-02T19:36:19,349 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/) 2022-06-02T19:36:19,350 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/) 2022-06-02T19:36:19,350 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/) 2022-06-02T19:36:19,351 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp34-cp34m-linux_armv7l.whl#sha256=30c2bb9cf26e969dbdc8978bd4710e9e8a42ee42ed7c9ad506c63a0855448307 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,351 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp34-cp34m-linux_armv6l.whl#sha256=527918d821e76043cda119ee29aa26b835f8f85251d560d47616e9147b5a1539 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,352 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp34-cp34m-linux_armv7l.whl#sha256=527918d821e76043cda119ee29aa26b835f8f85251d560d47616e9147b5a1539 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,352 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp35-cp35m-linux_armv6l.whl#sha256=b9d6e5734efb33b9383183904d491de8ef28aeeac7bbfdd617d48084126af113 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,353 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp35-cp35m-linux_armv7l.whl#sha256=b9d6e5734efb33b9383183904d491de8ef28aeeac7bbfdd617d48084126af113 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,353 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp39-cp39-linux_armv7l.whl#sha256=ef25ee9269f3b7f8ab95f1c3c563c39740fd2b7801df49d6be7e702c7db7f8fc (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,354 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp39-cp39-linux_armv6l.whl#sha256=ef25ee9269f3b7f8ab95f1c3c563c39740fd2b7801df49d6be7e702c7db7f8fc (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,354 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp35-cp35m-linux_armv7l.whl#sha256=46ca86446af4c56b5805a1cb36dd77ac64d009abb5500878ea4fa26320c7ba43 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,354 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp35-cp35m-linux_armv6l.whl#sha256=46ca86446af4c56b5805a1cb36dd77ac64d009abb5500878ea4fa26320c7ba43 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,355 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp34-cp34m-linux_armv6l.whl#sha256=89151b95fc0cd948f7a2d1d660b8c2453a612a752a2a2d7d8fb6d169ff2782d4 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,355 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp34-cp34m-linux_armv7l.whl#sha256=89151b95fc0cd948f7a2d1d660b8c2453a612a752a2a2d7d8fb6d169ff2782d4 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,356 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp37-cp37m-linux_armv7l.whl#sha256=a073eda71f157be82bd9b81ac12793e63834dde1ac9b63ca704668a88b025c1e (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,356 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp37-cp37m-linux_armv6l.whl#sha256=a073eda71f157be82bd9b81ac12793e63834dde1ac9b63ca704668a88b025c1e (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,357 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp35-cp35m-linux_armv7l.whl#sha256=47de147e5ee68a99b75107632aaa1e3bf84b4fa1f5bd7a456c1537266d437fbb (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,357 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp35-cp35m-linux_armv6l.whl#sha256=47de147e5ee68a99b75107632aaa1e3bf84b4fa1f5bd7a456c1537266d437fbb (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,358 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp34-cp34m-linux_armv6l.whl#sha256=a0ddeb70a574aee9a5c491f2da635dc26e5e5b2b4cac7d8abbbffb3c1b4c7a8a (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,358 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp34-cp34m-linux_armv7l.whl#sha256=a0ddeb70a574aee9a5c491f2da635dc26e5e5b2b4cac7d8abbbffb3c1b4c7a8a (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,359 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp35-cp35m-linux_armv6l.whl#sha256=28a9bbed8fd84f6ebdf4efb48ef9e2435715169ef7a558ad7f11a33232e83815 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,359 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp35-cp35m-linux_armv7l.whl#sha256=28a9bbed8fd84f6ebdf4efb48ef9e2435715169ef7a558ad7f11a33232e83815 (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,360 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp34-cp34m-linux_armv6l.whl#sha256=6d813f8dee5bde52fe344b851079bfaab34030f253869d7098ee33929566e36a (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,360 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp34-cp34m-linux_armv7l.whl#sha256=6d813f8dee5bde52fe344b851079bfaab34030f253869d7098ee33929566e36a (from https://www.piwheels.org/simple/mdanalysis/) 2022-06-02T19:36:19,361 Skipping link: not a file: https://www.piwheels.org/simple/mdanalysis/ 2022-06-02T19:36:19,361 Skipping link: not a file: https://pypi.org/simple/mdanalysis/ 2022-06-02T19:36:19,415 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates 2022-06-02T19:36:19,457 Collecting mdanalysis==2.2.0 2022-06-02T19:36:19,462 Created temporary directory: /tmp/pip-unpack-6489rq4f 2022-06-02T19:36:19,837 Downloading MDAnalysis-2.2.0.tar.gz (3.6 MB) 2022-06-02T19:36:23,777 Added mdanalysis==2.2.0 from https://files.pythonhosted.org/packages/5b/73/a077ff42d0cd88c5d3d6320fb156811cf67b28b5ea09a3c800e31af84b9b/MDAnalysis-2.2.0.tar.gz#sha256=bf9c9b7a03404e65aad66215d4c2ff8834ab747551eeaee059ff3e599a99d322 to build tracker '/tmp/pip-build-tracker-9e2zji9q' 2022-06-02T19:36:23,858 Created temporary directory: /tmp/pip-build-env-05kmec88 2022-06-02T19:36:23,879 Created temporary directory: /tmp/pip-standalone-pip-4u3gkkay 2022-06-02T19:36:26,301 Installing build dependencies: started 2022-06-02T19:36:26,304 Running command pip subprocess to install build dependencies 2022-06-02T19:36:37,496 Using pip 22.1 from /tmp/pip-standalone-pip-4u3gkkay/__env_pip__.zip/pip (python 3.9) 2022-06-02T19:36:38,999 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-06-02T19:36:39,003 Ignoring numpy: markers 'python_version == "3.8" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_machine != "aarch64"' don't match your environment 2022-06-02T19:36:39,006 Ignoring numpy: markers 'python_version == "3.10" and platform_python_implementation != "PyPy"' don't match your environment 2022-06-02T19:36:39,009 Ignoring numpy: markers 'python_version == "3.8" and platform_machine == "arm64" and platform_system == "Darwin"' don't match your environment 2022-06-02T19:36:39,011 Ignoring numpy: markers 'python_version == "3.9" and platform_machine == "arm64" and platform_system == "Darwin"' don't match your environment 2022-06-02T19:36:42,970 Collecting Cython>=0.28 2022-06-02T19:36:44,333 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.30-cp39-cp39-linux_armv7l.whl (5.0 MB) 2022-06-02T19:36:45,172 Collecting packaging 2022-06-02T19:36:45,206 Using cached https://www.piwheels.org/simple/packaging/packaging-21.3-py3-none-any.whl (40 kB) 2022-06-02T19:36:48,936 Collecting numpy==1.19.3 2022-06-02T19:36:51,169 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB) 2022-06-02T19:36:55,874 Collecting setuptools 2022-06-02T19:36:56,182 Using cached https://www.piwheels.org/simple/setuptools/setuptools-62.3.2-py3-none-any.whl (1.2 MB) 2022-06-02T19:36:56,837 Collecting wheel 2022-06-02T19:36:56,872 Using cached https://www.piwheels.org/simple/wheel/wheel-0.37.1-py2.py3-none-any.whl (35 kB) 2022-06-02T19:36:57,584 Collecting pyparsing!=3.0.5,>=2.0.2 2022-06-02T19:36:57,650 Using cached https://www.piwheels.org/simple/pyparsing/pyparsing-3.0.9-py3-none-any.whl (98 kB) 2022-06-02T19:37:01,845 Installing collected packages: wheel, setuptools, pyparsing, numpy, Cython, packaging 2022-06-02T19:37:02,135 Creating /tmp/pip-build-env-05kmec88/overlay/bin 2022-06-02T19:37:02,139 changing mode of /tmp/pip-build-env-05kmec88/overlay/bin/wheel to 755 2022-06-02T19:37:22,552 changing mode of /tmp/pip-build-env-05kmec88/overlay/bin/f2py to 755 2022-06-02T19:37:22,557 changing mode of /tmp/pip-build-env-05kmec88/overlay/bin/f2py3 to 755 2022-06-02T19:37:22,562 changing mode of /tmp/pip-build-env-05kmec88/overlay/bin/f2py3.9 to 755 2022-06-02T19:37:28,885 changing mode of /tmp/pip-build-env-05kmec88/overlay/bin/cygdb to 755 2022-06-02T19:37:28,889 changing mode of /tmp/pip-build-env-05kmec88/overlay/bin/cython to 755 2022-06-02T19:37:28,894 changing mode of /tmp/pip-build-env-05kmec88/overlay/bin/cythonize to 755 2022-06-02T19:37:29,207 Successfully installed Cython-0.29.30 numpy-1.19.3 packaging-21.3 pyparsing-3.0.9 setuptools-62.3.2 wheel-0.37.1 2022-06-02T19:37:29,406 WARNING: There was an error checking the latest version of pip. 2022-06-02T19:37:30,084 Installing build dependencies: finished with status 'done' 2022-06-02T19:37:30,132 Getting requirements to build wheel: started 2022-06-02T19:37:30,134 Running command Getting requirements to build wheel 2022-06-02T19:37:37,814 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-06-02T19:37:37,816 Will attempt to use Cython. 2022-06-02T19:37:38,296 Getting requirements to build wheel: finished with status 'done' 2022-06-02T19:37:38,328 Created temporary directory: /tmp/pip-modern-metadata-f85tx815 2022-06-02T19:37:38,334 Preparing metadata (pyproject.toml): started 2022-06-02T19:37:38,336 Running command Preparing metadata (pyproject.toml) 2022-06-02T19:37:43,262 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-06-02T19:37:43,264 Will attempt to use Cython. 2022-06-02T19:37:49,916 running dist_info 2022-06-02T19:37:50,539 creating /tmp/pip-modern-metadata-f85tx815/MDAnalysis.egg-info 2022-06-02T19:37:51,131 writing /tmp/pip-modern-metadata-f85tx815/MDAnalysis.egg-info/PKG-INFO 2022-06-02T19:37:51,694 writing dependency_links to /tmp/pip-modern-metadata-f85tx815/MDAnalysis.egg-info/dependency_links.txt 2022-06-02T19:37:54,484 writing requirements to /tmp/pip-modern-metadata-f85tx815/MDAnalysis.egg-info/requires.txt 2022-06-02T19:37:55,041 writing top-level names to /tmp/pip-modern-metadata-f85tx815/MDAnalysis.egg-info/top_level.txt 2022-06-02T19:37:55,044 writing manifest file '/tmp/pip-modern-metadata-f85tx815/MDAnalysis.egg-info/SOURCES.txt' 2022-06-02T19:37:56,413 reading manifest file '/tmp/pip-modern-metadata-f85tx815/MDAnalysis.egg-info/SOURCES.txt' 2022-06-02T19:37:56,416 reading manifest template 'MANIFEST.in' 2022-06-02T19:37:56,794 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2022-06-02T19:37:56,797 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2022-06-02T19:37:56,800 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2022-06-02T19:37:56,804 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2022-06-02T19:37:56,807 warning: no previously-included files matching '*~' found anywhere in distribution 2022-06-02T19:37:56,810 warning: no previously-included files matching '.git' found anywhere in distribution 2022-06-02T19:37:56,810 adding license file 'LICENSE' 2022-06-02T19:37:56,811 adding license file 'AUTHORS' 2022-06-02T19:37:56,850 writing manifest file '/tmp/pip-modern-metadata-f85tx815/MDAnalysis.egg-info/SOURCES.txt' 2022-06-02T19:37:56,854 creating '/tmp/pip-modern-metadata-f85tx815/MDAnalysis-2.2.0.dist-info' 2022-06-02T19:37:57,005 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2022-06-02T19:37:57,094 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-06-02T19:37:57,096 adding license file "AUTHORS" (matched pattern "AUTHORS*") 2022-06-02T19:37:57,473 Preparing metadata (pyproject.toml): finished with status 'done' 2022-06-02T19:37:57,489 Source in /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda has version 2.2.0, which satisfies requirement mdanalysis==2.2.0 from https://files.pythonhosted.org/packages/5b/73/a077ff42d0cd88c5d3d6320fb156811cf67b28b5ea09a3c800e31af84b9b/MDAnalysis-2.2.0.tar.gz#sha256=bf9c9b7a03404e65aad66215d4c2ff8834ab747551eeaee059ff3e599a99d322 2022-06-02T19:37:57,491 Removed mdanalysis==2.2.0 from https://files.pythonhosted.org/packages/5b/73/a077ff42d0cd88c5d3d6320fb156811cf67b28b5ea09a3c800e31af84b9b/MDAnalysis-2.2.0.tar.gz#sha256=bf9c9b7a03404e65aad66215d4c2ff8834ab747551eeaee059ff3e599a99d322 from build tracker '/tmp/pip-build-tracker-9e2zji9q' 2022-06-02T19:37:57,505 Created temporary directory: /tmp/pip-unpack-iom6z6nz 2022-06-02T19:37:57,506 Building wheels for collected packages: mdanalysis 2022-06-02T19:37:57,516 Created temporary directory: /tmp/pip-wheel-4ah551iu 2022-06-02T19:37:57,517 Destination directory: /tmp/pip-wheel-4ah551iu 2022-06-02T19:37:57,521 Building wheel for mdanalysis (pyproject.toml): started 2022-06-02T19:37:57,524 Running command Building wheel for mdanalysis (pyproject.toml) 2022-06-02T19:38:02,461 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2022-06-02T19:38:02,462 Will attempt to use Cython. 2022-06-02T19:38:08,624 running bdist_wheel 2022-06-02T19:38:08,690 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2022-06-02T19:38:09,320 running build 2022-06-02T19:38:09,321 running build_py 2022-06-02T19:38:09,913 creating build 2022-06-02T19:38:09,913 creating build/lib.linux-armv7l-cpython-39 2022-06-02T19:38:09,915 creating build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-06-02T19:38:09,917 copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-06-02T19:38:09,921 copying MDAnalysis/due.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-06-02T19:38:09,925 copying MDAnalysis/authors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-06-02T19:38:09,928 copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-06-02T19:38:09,932 copying MDAnalysis/units.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-06-02T19:38:09,937 copying MDAnalysis/version.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2022-06-02T19:38:09,943 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,945 copying MDAnalysis/transformations/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,949 copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,953 copying MDAnalysis/transformations/wrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,958 copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,961 copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,966 copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,970 copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,975 copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2022-06-02T19:38:09,982 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-06-02T19:38:09,984 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-06-02T19:38:09,988 copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-06-02T19:38:09,992 copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-06-02T19:38:09,995 copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-06-02T19:38:09,999 copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-06-02T19:38:10,003 copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-06-02T19:38:10,007 copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2022-06-02T19:38:10,014 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,016 copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,022 copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,027 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,031 copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,040 copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,044 copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,048 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,054 copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,059 copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,064 copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,068 copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,072 copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,077 copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,082 copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,087 copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,090 copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,097 copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,101 copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,106 copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,111 copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,120 copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,123 copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,127 copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,132 copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,139 copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,144 copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,147 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,151 copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,155 copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,163 copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,167 copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,172 copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2022-06-02T19:38:10,179 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,181 copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,186 copying MDAnalysis/lib/correlations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,190 copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,193 copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,202 copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,211 copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,215 copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,219 copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,230 copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,234 copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,242 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,286 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,290 copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,295 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,300 copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,306 copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,310 copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,318 copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,324 copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,328 copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,333 copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,336 copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,342 copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,347 copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,353 copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,361 copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,365 copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,369 copying MDAnalysis/analysis/bat.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,374 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,380 copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,384 copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,390 copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,394 copying MDAnalysis/analysis/msd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,399 copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:38:10,404 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2022-06-02T19:38:10,406 copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2022-06-02T19:38:10,411 copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2022-06-02T19:38:10,414 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2022-06-02T19:38:10,421 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-06-02T19:38:10,423 copying MDAnalysis/converters/RDKit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-06-02T19:38:10,429 copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-06-02T19:38:10,433 copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-06-02T19:38:10,437 copying MDAnalysis/converters/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-06-02T19:38:10,440 copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-06-02T19:38:10,445 copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-06-02T19:38:10,449 copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2022-06-02T19:38:10,457 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,459 copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,463 copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,466 copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,470 copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,474 copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,477 copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,480 copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,484 copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,488 copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,493 copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,497 copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,501 copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,504 copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,509 copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,513 copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,517 copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,521 copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,525 copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,529 copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,533 copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,537 copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,543 copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,547 copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,551 copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,555 copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,560 copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,564 copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,569 copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2022-06-02T19:38:10,574 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2022-06-02T19:38:10,575 copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2022-06-02T19:38:10,579 copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2022-06-02T19:38:10,584 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,586 copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,593 copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,600 copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,604 copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,608 copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,621 copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,625 copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,634 copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,638 copying MDAnalysis/core/accessors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2022-06-02T19:38:10,644 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-06-02T19:38:10,645 copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-06-02T19:38:10,651 copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-06-02T19:38:10,655 copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-06-02T19:38:10,659 copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2022-06-02T19:38:10,664 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-06-02T19:38:10,665 copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-06-02T19:38:10,670 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2022-06-02T19:38:10,672 copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2022-06-02T19:38:10,677 copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2022-06-02T19:38:10,682 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-06-02T19:38:10,683 copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-06-02T19:38:10,686 copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-06-02T19:38:10,692 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:38:10,693 copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:38:10,702 copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:38:10,707 copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:38:10,711 copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:38:10,719 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-06-02T19:38:10,720 copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-06-02T19:38:10,731 copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-06-02T19:38:10,736 copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-06-02T19:38:10,740 copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-06-02T19:38:10,744 copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-06-02T19:38:10,748 copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-06-02T19:38:10,754 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-06-02T19:38:10,755 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-06-02T19:38:10,763 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-06-02T19:38:10,767 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-06-02T19:38:10,771 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2022-06-02T19:38:10,777 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2022-06-02T19:38:10,779 copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2022-06-02T19:38:10,782 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2022-06-02T19:38:10,787 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-06-02T19:38:10,789 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-06-02T19:38:10,793 copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-06-02T19:38:10,797 copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-06-02T19:38:10,801 copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-06-02T19:38:10,807 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:38:10,808 copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:38:10,813 copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:38:10,817 copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:38:10,822 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-06-02T19:38:10,824 copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-06-02T19:38:10,830 copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-06-02T19:38:10,833 copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-06-02T19:38:10,837 copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2022-06-02T19:38:10,846 copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-06-02T19:38:10,855 copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2022-06-02T19:38:10,897 running build_ext 2022-06-02T19:38:10,901 building 'MDAnalysis.lib.formats.libdcd' extension 2022-06-02T19:38:10,902 creating build/temp.linux-armv7l-cpython-39 2022-06-02T19:38:10,903 creating build/temp.linux-armv7l-cpython-39/MDAnalysis 2022-06-02T19:38:10,904 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib 2022-06-02T19:38:10,905 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2022-06-02T19:38:10,907 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-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:38:10,979 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:38:11,824 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:38:11,825 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:38:11,825 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:38:11,826 from MDAnalysis/lib/formats/libdcd.c:728: 2022-06-02T19:38:11,826 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:38:11,826 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:38:11,827 | ^~~~~~~ 2022-06-02T19:38:12,034 In file included from MDAnalysis/lib/formats/libdcd.c:737: 2022-06-02T19:38:12,035 MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’: 2022-06-02T19:38:12,036 MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-06-02T19:38:12,036 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2022-06-02T19:38:12,037 | ^~ 2022-06-02T19:38:12,045 MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’: 2022-06-02T19:38:12,046 MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable] 2022-06-02T19:38:12,046 698 | struct tm *tmbuf; 2022-06-02T19:38:12,047 | ^~~~~ 2022-06-02T19:38:12,048 MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable] 2022-06-02T19:38:12,048 697 | time_t cur_time; 2022-06-02T19:38:12,049 | ^~~~~~~~ 2022-06-02T19:38:17,634 In file included from MDAnalysis/lib/formats/include/readdcd.h:25, 2022-06-02T19:38:17,634 from MDAnalysis/lib/formats/libdcd.c:737: 2022-06-02T19:38:17,635 At top level: 2022-06-02T19:38:17,636 MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2022-06-02T19:38:17,636 96 | static void swap2_aligned(void *v, long ndata) { 2022-06-02T19:38:17,637 | ^~~~~~~~~~~~~ 2022-06-02T19:38:17,637 MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2022-06-02T19:38:17,638 32 | static void swap2_unaligned(void *v, long ndata) { 2022-06-02T19:38:17,638 | ^~~~~~~~~~~~~~~ 2022-06-02T19:38:17,639 In file included from MDAnalysis/lib/formats/libdcd.c:736: 2022-06-02T19:38:17,639 MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2022-06-02T19:38:17,639 453 | static int fio_write_str(fio_fd fd, const char *str) { 2022-06-02T19:38:17,640 | ^~~~~~~~~~~~~ 2022-06-02T19:38:17,640 MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2022-06-02T19:38:17,641 449 | static int fio_read_int32(fio_fd fd, int *i) { 2022-06-02T19:38:17,641 | ^~~~~~~~~~~~~~ 2022-06-02T19:39:35,281 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:39:35,788 building 'MDAnalysis.lib.c_distances' extension 2022-06-02T19:39:35,790 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:39:35,862 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:39:36,624 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:39:36,625 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:39:36,625 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:39:36,626 from MDAnalysis/lib/c_distances.c:730: 2022-06-02T19:39:36,626 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:39:36,627 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:39:36,627 | ^~~~~~~ 2022-06-02T19:40:47,353 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:40:47,905 building 'MDAnalysis.lib.c_distances_openmp' extension 2022-06-02T19:40:47,907 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:40:47,971 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:40:48,709 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:40:48,709 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:40:48,709 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:40:48,710 from MDAnalysis/lib/c_distances_openmp.c:741: 2022-06-02T19:40:48,710 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:40:48,710 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:40:48,711 | ^~~~~~~ 2022-06-02T19:41:02,305 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib -lm -lgomp -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -fopenmp 2022-06-02T19:41:02,682 building 'MDAnalysis.lib.qcprot' extension 2022-06-02T19:41:02,684 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:41:02,744 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:41:03,442 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:41:03,443 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:41:03,443 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:41:03,444 from MDAnalysis/lib/qcprot.c:724: 2022-06-02T19:41:03,444 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:41:03,444 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:41:03,445 | ^~~~~~~ 2022-06-02T19:41:03,572 MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’: 2022-06-02T19:41:03,574 MDAnalysis/lib/qcprot.c:2362:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:41:03,574 2362 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2022-06-02T19:41:03,574 | ^ 2022-06-02T19:41:03,582 MDAnalysis/lib/qcprot.c:2570:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:41:03,583 2570 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2022-06-02T19:41:03,583 | ^ 2022-06-02T19:41:17,229 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:41:17,506 building 'MDAnalysis.lib._transformations' extension 2022-06-02T19:41:17,508 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src 2022-06-02T19:41:17,509 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2022-06-02T19:41:17,511 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:41:17,567 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:41:18,256 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:41:18,256 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:41:18,257 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:41:18,257 from MDAnalysis/lib/src/transformations/transformations.c:73: 2022-06-02T19:41:18,257 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:41:18,258 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:41:18,258 | ^~~~~~~ 2022-06-02T19:41:18,404 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: 2022-06-02T19:41:18,405 MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,405 1845 | #pragma vector always 2022-06-02T19:41:18,406 | 2022-06-02T19:41:18,411 MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,411 1962 | #pragma vector always 2022-06-02T19:41:18,411 | 2022-06-02T19:41:18,413 MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,413 1986 | #pragma vector always 2022-06-02T19:41:18,413 | 2022-06-02T19:41:18,421 MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: 2022-06-02T19:41:18,423 MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] 2022-06-02T19:41:18,424 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { 2022-06-02T19:41:18,424 | ^~ 2022-06-02T19:41:18,424 In file included from /usr/include/python3.9/Python.h:97, 2022-06-02T19:41:18,425 from MDAnalysis/lib/src/transformations/transformations.c:68: 2022-06-02T19:41:18,425 /usr/include/python3.9/unicodeobject.h:177:43: note: declared here 2022-06-02T19:41:18,425 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( 2022-06-02T19:41:18,426 | ^~~~~~~~~~~~~~~~~ 2022-06-02T19:41:18,516 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: 2022-06-02T19:41:18,517 MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,518 3427 | #pragma vector always 2022-06-02T19:41:18,518 | 2022-06-02T19:41:18,523 MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,524 3508 | #pragma vector always 2022-06-02T19:41:18,524 | 2022-06-02T19:41:18,537 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: 2022-06-02T19:41:18,538 MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,538 3610 | #pragma vector always 2022-06-02T19:41:18,539 | 2022-06-02T19:41:18,539 MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,540 3615 | #pragma vector always 2022-06-02T19:41:18,540 | 2022-06-02T19:41:18,550 MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,550 3679 | #pragma vector always 2022-06-02T19:41:18,550 | 2022-06-02T19:41:18,551 MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2022-06-02T19:41:18,551 3684 | #pragma vector always 2022-06-02T19:41:18,551 | 2022-06-02T19:41:18,715 At top level: 2022-06-02T19:41:18,716 MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] 2022-06-02T19:41:18,716 910 | PyConverter_DoubleVector4Copy( 2022-06-02T19:41:18,716 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:41:18,717 MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] 2022-06-02T19:41:18,717 804 | PyConverter_DoubleArrayOrNone( 2022-06-02T19:41:18,717 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:41:18,718 MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] 2022-06-02T19:41:18,718 774 | PyConverter_DoubleArray( 2022-06-02T19:41:18,718 | ^~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:41:32,552 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:41:32,835 building 'MDAnalysis.lib.formats.libmdaxdr' extension 2022-06-02T19:41:32,837 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2022-06-02T19:41:32,840 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-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:41:32,911 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:41:33,601 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:41:33,602 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:41:33,602 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:41:33,603 from MDAnalysis/lib/formats/libmdaxdr.c:751: 2022-06-02T19:41:33,603 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:41:33,603 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:41:33,604 | ^~~~~~~ 2022-06-02T19:41:33,675 In file included from MDAnalysis/lib/formats/libmdaxdr.c:757: 2022-06-02T19:41:33,676 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:41:33,676 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:41:33,677 | 2022-06-02T19:41:33,679 In file included from MDAnalysis/lib/formats/libmdaxdr.c:758: 2022-06-02T19:41:33,679 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:41:33,680 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:41:33,680 | 2022-06-02T19:41:33,680 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2022-06-02T19:41:33,681 from MDAnalysis/lib/formats/libmdaxdr.c:758: 2022-06-02T19:41:33,681 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:41:33,681 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:41:33,682 | 2022-06-02T19:41:33,682 In file included from MDAnalysis/lib/formats/libmdaxdr.c:759: 2022-06-02T19:41:33,682 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:41:33,683 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:41:33,683 | 2022-06-02T19:42:46,131 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:42:46,194 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:42:46,324 In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: 2022-06-02T19:42:46,325 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:46,325 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:46,325 | 2022-06-02T19:42:46,338 In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: 2022-06-02T19:42:46,339 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:46,339 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:46,339 | 2022-06-02T19:42:46,340 In file included from /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2022-06-02T19:42:46,341 from MDAnalysis/lib/formats/src/trr_seek.c:31: 2022-06-02T19:42:46,341 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:46,341 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:46,342 | 2022-06-02T19:42:46,348 MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’: 2022-06-02T19:42:46,349 MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable] 2022-06-02T19:42:46,350 39 | int result, framebytes, totalframebytes; 2022-06-02T19:42:46,350 | ^~~~~~~~~~~~~~~ 2022-06-02T19:42:46,351 MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable] 2022-06-02T19:42:46,351 38 | float time, lambda; 2022-06-02T19:42:46,351 | ^~~~~~ 2022-06-02T19:42:46,351 MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable] 2022-06-02T19:42:46,352 38 | float time, lambda; 2022-06-02T19:42:46,352 | ^~~~ 2022-06-02T19:42:46,602 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-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:42:46,657 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:42:46,893 In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: 2022-06-02T19:42:46,893 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:46,894 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:46,894 | 2022-06-02T19:42:46,915 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’: 2022-06-02T19:42:46,916 MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-06-02T19:42:46,916 501 | while (size >= num && num_of_bits < 32) 2022-06-02T19:42:46,917 | ^~ 2022-06-02T19:42:46,918 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’: 2022-06-02T19:42:46,919 MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:42:46,920 547 | while (bytes[num_of_bytes] >= num) 2022-06-02T19:42:46,920 | ^~ 2022-06-02T19:42:46,923 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’: 2022-06-02T19:42:46,924 MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-06-02T19:42:46,925 656 | if (num_of_bits >= num_of_bytes * 8) 2022-06-02T19:42:46,925 | ^~ 2022-06-02T19:42:46,926 MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-06-02T19:42:46,926 658 | for (i = 0; i < num_of_bytes; i++) 2022-06-02T19:42:46,927 | ^ 2022-06-02T19:42:46,928 MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-06-02T19:42:46,928 666 | for (i = 0; i < num_of_bytes-1; i++) 2022-06-02T19:42:46,929 | ^ 2022-06-02T19:42:46,930 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’: 2022-06-02T19:42:46,931 MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:42:46,931 706 | if (lastbits < num_of_bits) 2022-06-02T19:42:46,932 | ^ 2022-06-02T19:42:46,936 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2022-06-02T19:42:46,936 MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:42:46,937 816 | if(size3>xfp->buf1size) 2022-06-02T19:42:46,937 | ^ 2022-06-02T19:42:46,940 MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:42:46,940 868 | maxidx = (LASTIDXxfp->buf1size) 2022-06-02T19:42:46,950 | ^ 2022-06-02T19:42:46,959 MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-06-02T19:42:46,960 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2022-06-02T19:42:46,960 | ^ 2022-06-02T19:42:46,961 MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:42:46,961 1141 | maxidx = (LASTIDXxfp->buf1size) 2022-06-02T19:42:46,974 | ^ 2022-06-02T19:42:46,978 MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:42:46,978 1368 | maxidx = (LASTIDXxfp->buf1size) { 2022-06-02T19:42:46,993 | ^ 2022-06-02T19:42:47,006 MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2022-06-02T19:42:47,007 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2022-06-02T19:42:47,007 | ^ 2022-06-02T19:42:47,008 MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2022-06-02T19:42:47,009 1624 | maxidx = (LASTIDX maxsize) 2022-06-02T19:42:51,018 | ^ 2022-06-02T19:42:51,021 MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here 2022-06-02T19:42:51,021 2335 | unsigned int size; 2022-06-02T19:42:51,021 | ^~~~ 2022-06-02T19:42:52,065 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2022-06-02T19:42:52,066 MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-06-02T19:42:52,066 1157 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2022-06-02T19:42:52,066 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-06-02T19:42:52,067 MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-06-02T19:42:52,068 1156 | abs(thiscoord[1] - prevcoord[1]) < larger && 2022-06-02T19:42:52,068 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-06-02T19:42:52,069 MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-06-02T19:42:52,069 1155 | abs(thiscoord[0] - prevcoord[0]) < larger && 2022-06-02T19:42:52,069 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-06-02T19:42:53,887 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2022-06-02T19:42:53,888 MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-06-02T19:42:53,889 1639 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2022-06-02T19:42:53,889 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-06-02T19:42:53,890 MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-06-02T19:42:53,891 1638 | abs(thiscoord[1] - prevcoord[1]) < larger && 2022-06-02T19:42:53,891 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-06-02T19:42:53,892 MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-06-02T19:42:53,893 1637 | abs(thiscoord[0] - prevcoord[0]) < larger && 2022-06-02T19:42:53,893 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2022-06-02T19:42:56,323 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-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:42:56,378 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:42:56,496 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: 2022-06-02T19:42:56,496 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:56,496 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:56,497 | 2022-06-02T19:42:56,505 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2022-06-02T19:42:56,506 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:56,506 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:56,506 | 2022-06-02T19:42:56,507 In file included from /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2022-06-02T19:42:56,507 from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2022-06-02T19:42:56,507 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:56,508 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:56,508 | 2022-06-02T19:42:56,510 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’: 2022-06-02T19:42:56,510 MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-02T19:42:56,511 78 | if (slen != strlen(version) + 1) 2022-06-02T19:42:56,511 | ^~ 2022-06-02T19:42:56,512 MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2022-06-02T19:42:56,512 86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) 2022-06-02T19:42:56,512 | ^~ 2022-06-02T19:42:56,549 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’: 2022-06-02T19:42:56,549 MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized] 2022-06-02T19:42:56,550 408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); 2022-06-02T19:42:56,550 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:42:59,127 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-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:42:59,182 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:42:59,241 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: 2022-06-02T19:42:59,241 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:59,242 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:59,242 | 2022-06-02T19:42:59,271 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2022-06-02T19:42:59,271 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:59,272 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:59,272 | 2022-06-02T19:42:59,273 In file included from /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2022-06-02T19:42:59,273 from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2022-06-02T19:42:59,273 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:59,274 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:59,274 | 2022-06-02T19:42:59,566 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-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:42:59,621 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:42:59,676 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: 2022-06-02T19:42:59,677 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:59,677 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:59,677 | 2022-06-02T19:42:59,704 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2022-06-02T19:42:59,704 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:59,705 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:59,705 | 2022-06-02T19:42:59,706 In file included from /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2022-06-02T19:42:59,707 from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2022-06-02T19:42:59,707 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2022-06-02T19:42:59,707 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2022-06-02T19:42:59,707 | 2022-06-02T19:43:00,085 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:43:00,622 building 'MDAnalysis.lib.formats.cython_util' extension 2022-06-02T19:43:00,624 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2022-06-02T19:43:00,688 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:43:01,397 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:43:01,397 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:43:01,398 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:43:01,398 from MDAnalysis/lib/formats/cython_util.c:724: 2022-06-02T19:43:01,398 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:43:01,399 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:43:01,399 | ^~~~~~~ 2022-06-02T19:43:40,927 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:43:41,289 building 'MDAnalysis.analysis.encore.cutils' extension 2022-06-02T19:43:41,291 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis 2022-06-02T19:43:41,292 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2022-06-02T19:43:41,295 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-06-02T19:43:41,353 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:43:42,050 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:43:42,051 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:43:42,051 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:43:42,051 from MDAnalysis/analysis/encore/cutils.c:724: 2022-06-02T19:43:42,051 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:43:42,052 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:43:42,052 | ^~~~~~~ 2022-06-02T19:43:48,302 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:43:48,555 building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension 2022-06-02T19:43:48,557 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2022-06-02T19:43:48,558 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2022-06-02T19:43:48,560 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-06-02T19:43:48,623 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:43:49,322 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:43:49,323 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:43:49,323 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:43:49,323 from MDAnalysis/analysis/encore/clustering/affinityprop.c:730: 2022-06-02T19:43:49,324 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:43:49,324 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:43:49,324 | ^~~~~~~ 2022-06-02T19:44:13,095 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-06-02T19:44:13,151 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:44:15,555 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:44:15,898 building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension 2022-06-02T19:44:15,900 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:44:15,900 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2022-06-02T19:44:15,903 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-06-02T19:44:15,958 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:44:17,587 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2022-06-02T19:44:17,645 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:44:18,346 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:44:18,346 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:44:18,347 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:44:18,347 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:730: 2022-06-02T19:44:18,347 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:44:18,348 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:44:18,348 | ^~~~~~~ 2022-06-02T19:44:28,661 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:44:28,949 building 'MDAnalysis.lib._cutil' extension 2022-06-02T19:44:28,952 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2022-06-02T19:44:29,021 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:44:29,578 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:44:29,578 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:44:29,578 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:44:29,579 from MDAnalysis/lib/_cutil.cpp:744: 2022-06-02T19:44:29,579 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:44:29,579 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:44:29,580 | ^~~~~~~ 2022-06-02T19:44:36,344 In file included from MDAnalysis/lib/_cutil.cpp:770: 2022-06-02T19:44:36,344 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:856:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,345 856 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,345 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,345 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:820:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,346 820 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,346 | ^~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,347 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:792:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,347 792 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,347 | ^~~~~~~~~~~~~~ 2022-06-02T19:44:36,348 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:715:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,348 715 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,349 | ^~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,349 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:672:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,349 672 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,350 | ^~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,350 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:641:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,351 641 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,351 | ^~~~~~~~~~~ 2022-06-02T19:44:36,351 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:616:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,352 616 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,352 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,352 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:591:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,353 591 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,353 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,353 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:572:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,354 572 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2022-06-02T19:44:36,354 | ^~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,354 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:517:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,354 517 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2022-06-02T19:44:36,355 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,355 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:484:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,355 484 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2022-06-02T19:44:36,356 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,356 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:457:13: warning: ‘void _calc_self_distance_array(float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,356 457 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2022-06-02T19:44:36,357 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,357 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:430:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,357 430 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2022-06-02T19:44:36,358 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,358 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:403:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,358 403 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2022-06-02T19:44:36,358 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,359 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:382:13: warning: ‘void _calc_distance_array(float (*)[3], uint64_t, float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,359 382 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2022-06-02T19:44:36,359 | ^~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:44:36,360 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:111:13: warning: ‘void _ortho_pbc(float (*)[3], uint64_t, float*)’ defined but not used [-Wunused-function] 2022-06-02T19:44:36,360 111 | static void _ortho_pbc(coordinate* coords, uint64_t numcoords, float* box) 2022-06-02T19:44:36,360 | ^~~~~~~~~~ 2022-06-02T19:45:37,565 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:45:38,375 building 'MDAnalysis.lib._augment' extension 2022-06-02T19:45:38,377 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2022-06-02T19:45:38,451 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:45:39,017 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2022-06-02T19:45:39,018 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2022-06-02T19:45:39,019 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2022-06-02T19:45:39,019 from MDAnalysis/lib/_augment.cpp:739: 2022-06-02T19:45:39,019 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2022-06-02T19:45:39,020 17 | #warning "Using deprecated NumPy API, disable it with " \ 2022-06-02T19:45:39,020 | ^~~~~~~ 2022-06-02T19:46:37,699 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:46:38,406 building 'MDAnalysis.lib.nsgrid' extension 2022-06-02T19:46:38,409 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2022-06-02T19:46:38,483 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2022-06-02T19:46:44,183 In file included from MDAnalysis/lib/nsgrid.cpp:743: 2022-06-02T19:46:44,183 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:856:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,184 856 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,184 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,185 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:820:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,185 820 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,185 | ^~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,186 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:792:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,186 792 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,187 | ^~~~~~~~~~~~~~ 2022-06-02T19:46:44,187 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:715:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,187 715 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,188 | ^~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,188 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:672:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,188 672 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,189 | ^~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,189 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:641:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,189 641 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,190 | ^~~~~~~~~~~ 2022-06-02T19:46:44,190 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:616:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,190 616 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,191 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,191 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:591:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,191 591 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,191 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,192 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:572:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,192 572 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2022-06-02T19:46:44,193 | ^~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,193 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:517:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,193 517 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2022-06-02T19:46:44,193 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,194 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:484:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,194 484 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2022-06-02T19:46:44,194 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,195 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:457:13: warning: ‘void _calc_self_distance_array(float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,195 457 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2022-06-02T19:46:44,195 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,196 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:430:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,196 430 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2022-06-02T19:46:44,196 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,197 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:403:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,197 403 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2022-06-02T19:46:44,197 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:46:44,198 /tmp/pip-wheel-ciulgnpj/mdanalysis_dfc7e8b6c6e245a9a46e0d4e84abceda/MDAnalysis/lib/include/calc_distances.h:382:13: warning: ‘void _calc_distance_array(float (*)[3], uint64_t, float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2022-06-02T19:46:44,198 382 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2022-06-02T19:46:44,198 | ^~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:47:37,012 In file included from /usr/include/c++/10/vector:72, 2022-06-02T19:47:37,012 from MDAnalysis/lib/nsgrid.cpp:741: 2022-06-02T19:47:37,013 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2022-06-02T19:47:37,013 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-02T19:47:37,013 426 | vector<_Tp, _Alloc>:: 2022-06-02T19:47:37,014 | ^~~~~~~~~~~~~~~~~~~ 2022-06-02T19:47:37,100 In file included from /usr/include/c++/10/vector:67, 2022-06-02T19:47:37,100 from MDAnalysis/lib/nsgrid.cpp:741: 2022-06-02T19:47:37,101 /usr/include/c++/10/bits/stl_vector.h: In function ‘void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_add_neighbors(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, int, int, double)’: 2022-06-02T19:47:37,101 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-02T19:47:37,101 1198 | _M_realloc_insert(end(), __x); 2022-06-02T19:47:37,102 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-06-02T19:47:37,189 In file included from /usr/include/c++/10/vector:72, 2022-06-02T19:47:37,189 from MDAnalysis/lib/nsgrid.cpp:741: 2022-06-02T19:47:37,190 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2022-06-02T19:47:37,190 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-06-02T19:47:37,190 426 | vector<_Tp, _Alloc>:: 2022-06-02T19:47:37,191 | ^~~~~~~~~~~~~~~~~~~ 2022-06-02T19:47:37,778 /usr/include/c++/10/bits/vector.tcc: In function ‘PyObject* __pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults__set_state(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, PyObject*)’: 2022-06-02T19:47:37,778 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-06-02T19:47:37,779 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-06-02T19:47:37,779 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-06-02T19:47:45,301 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so 2022-06-02T19:47:47,314 installing to build/bdist.linux-armv7l/wheel 2022-06-02T19:47:47,314 running install 2022-06-02T19:47:47,377 running install_lib 2022-06-02T19:47:47,967 creating build/bdist.linux-armv7l 2022-06-02T19:47:47,967 creating build/bdist.linux-armv7l/wheel 2022-06-02T19:47:47,970 creating build/bdist.linux-armv7l/wheel/MDAnalysis 2022-06-02T19:47:47,973 creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:47,975 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:47,979 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:47,983 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/wrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:47,987 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:47,991 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:47,995 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:47,999 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:48,003 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2022-06-02T19:47:48,007 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-06-02T19:47:48,011 creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-06-02T19:47:48,013 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-06-02T19:47:48,017 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-06-02T19:47:48,021 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-06-02T19:47:48,024 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-06-02T19:47:48,028 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-06-02T19:47:48,031 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-06-02T19:47:48,034 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2022-06-02T19:47:48,038 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-06-02T19:47:48,041 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-06-02T19:47:48,046 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,047 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,052 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,056 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,060 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,068 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,073 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,076 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,080 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,085 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,090 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,094 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,099 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,104 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,108 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,113 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,116 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,121 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,125 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,130 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,135 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,143 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,146 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,149 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,154 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,160 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,164 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,167 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,171 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,175 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,182 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,186 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,190 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2022-06-02T19:47:48,196 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,198 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,216 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-06-02T19:47:48,218 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-06-02T19:47:48,274 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-06-02T19:47:48,382 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-06-02T19:47:48,385 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2022-06-02T19:47:48,489 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,516 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,537 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,542 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,636 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/correlations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,640 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,643 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,744 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,752 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,760 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,764 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,836 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,840 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,848 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,852 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,856 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2022-06-02T19:47:48,943 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-06-02T19:47:48,947 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-06-02T19:47:48,953 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:48,955 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:48,960 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2022-06-02T19:47:48,962 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2022-06-02T19:47:48,968 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2022-06-02T19:47:48,972 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-06-02T19:47:48,974 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-06-02T19:47:48,976 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-06-02T19:47:48,984 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-06-02T19:47:48,988 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2022-06-02T19:47:48,994 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:48,999 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,003 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,009 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,013 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,020 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,026 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,031 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,038 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:47:49,039 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:47:49,051 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:47:49,056 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:47:49,059 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2022-06-02T19:47:49,066 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,069 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,075 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,080 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,085 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,093 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,097 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,101 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/bat.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,105 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,110 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,117 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-06-02T19:47:49,119 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-06-02T19:47:49,121 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-06-02T19:47:49,126 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-06-02T19:47:49,129 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-06-02T19:47:49,133 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-06-02T19:47:49,160 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2022-06-02T19:47:49,164 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-06-02T19:47:49,172 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-06-02T19:47:49,176 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-06-02T19:47:49,181 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-06-02T19:47:49,184 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-06-02T19:47:49,201 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:47:49,202 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:47:49,206 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:47:49,211 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:47:49,214 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2022-06-02T19:47:49,234 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-06-02T19:47:49,238 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2022-06-02T19:47:49,242 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,248 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,253 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/msd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,259 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-06-02T19:47:49,260 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-06-02T19:47:49,268 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-06-02T19:47:49,272 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-06-02T19:47:49,276 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2022-06-02T19:47:49,282 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2022-06-02T19:47:49,283 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2022-06-02T19:47:49,287 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2022-06-02T19:47:49,290 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2022-06-02T19:47:49,295 creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2022-06-02T19:47:49,297 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2022-06-02T19:47:49,303 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2022-06-02T19:47:49,306 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2022-06-02T19:47:49,313 creating build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-06-02T19:47:49,314 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-06-02T19:47:49,321 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-06-02T19:47:49,326 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-06-02T19:47:49,330 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-06-02T19:47:49,333 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-06-02T19:47:49,337 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-06-02T19:47:49,342 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2022-06-02T19:47:49,348 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,349 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,354 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,357 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,361 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,364 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,367 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,371 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,374 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,378 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,382 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,386 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,390 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,393 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,397 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,401 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,406 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,411 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-06-02T19:47:49,412 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-06-02T19:47:49,418 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-06-02T19:47:49,421 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-06-02T19:47:49,425 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2022-06-02T19:47:49,429 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,433 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,437 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,441 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,445 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,450 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,454 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,458 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,462 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,467 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,471 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,476 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2022-06-02T19:47:49,480 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2022-06-02T19:47:49,484 creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2022-06-02T19:47:49,486 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2022-06-02T19:47:49,489 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2022-06-02T19:47:49,493 creating build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,495 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,502 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,509 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,515 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,519 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,531 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,536 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,545 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,550 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/accessors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2022-06-02T19:47:49,555 creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-06-02T19:47:49,557 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-06-02T19:47:49,564 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-06-02T19:47:49,569 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-06-02T19:47:49,573 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2022-06-02T19:47:49,577 running install_egg_info 2022-06-02T19:47:50,787 running egg_info 2022-06-02T19:47:51,374 writing MDAnalysis.egg-info/PKG-INFO 2022-06-02T19:47:51,931 writing dependency_links to MDAnalysis.egg-info/dependency_links.txt 2022-06-02T19:47:54,699 writing requirements to MDAnalysis.egg-info/requires.txt 2022-06-02T19:47:55,254 writing top-level names to MDAnalysis.egg-info/top_level.txt 2022-06-02T19:47:55,391 reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2022-06-02T19:47:55,482 reading manifest template 'MANIFEST.in' 2022-06-02T19:47:56,025 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2022-06-02T19:47:56,031 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2022-06-02T19:47:56,036 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2022-06-02T19:47:56,041 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2022-06-02T19:47:56,047 warning: no previously-included files matching '*~' found anywhere in distribution 2022-06-02T19:47:56,051 warning: no previously-included files matching '.git' found anywhere in distribution 2022-06-02T19:47:56,051 adding license file 'LICENSE' 2022-06-02T19:47:56,052 adding license file 'AUTHORS' 2022-06-02T19:47:56,106 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2022-06-02T19:47:56,111 Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-2.2.0-py3.9.egg-info 2022-06-02T19:47:56,135 running install_scripts 2022-06-02T19:47:56,312 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-06-02T19:47:56,314 adding license file "AUTHORS" (matched pattern "AUTHORS*") 2022-06-02T19:47:56,371 creating build/bdist.linux-armv7l/wheel/MDAnalysis-2.2.0.dist-info/WHEEL 2022-06-02T19:47:56,381 creating '/tmp/pip-wheel-4ah551iu/tmpgybfrp7e/MDAnalysis-2.2.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-06-02T19:47:56,386 adding 'MDAnalysis/__init__.py' 2022-06-02T19:47:56,389 adding 'MDAnalysis/authors.py' 2022-06-02T19:47:56,392 adding 'MDAnalysis/due.py' 2022-06-02T19:47:56,394 adding 'MDAnalysis/exceptions.py' 2022-06-02T19:47:56,399 adding 'MDAnalysis/units.py' 2022-06-02T19:47:56,402 adding 'MDAnalysis/version.py' 2022-06-02T19:47:56,406 adding 'MDAnalysis/analysis/__init__.py' 2022-06-02T19:47:56,425 adding 'MDAnalysis/analysis/align.py' 2022-06-02T19:47:56,433 adding 'MDAnalysis/analysis/base.py' 2022-06-02T19:47:56,440 adding 'MDAnalysis/analysis/bat.py' 2022-06-02T19:47:56,447 adding 'MDAnalysis/analysis/contacts.py' 2022-06-02T19:47:56,458 adding 'MDAnalysis/analysis/density.py' 2022-06-02T19:47:56,462 adding 'MDAnalysis/analysis/dielectric.py' 2022-06-02T19:47:56,468 adding 'MDAnalysis/analysis/diffusionmap.py' 2022-06-02T19:47:56,475 adding 'MDAnalysis/analysis/dihedrals.py' 2022-06-02T19:47:56,479 adding 'MDAnalysis/analysis/distances.py' 2022-06-02T19:47:56,484 adding 'MDAnalysis/analysis/gnm.py' 2022-06-02T19:47:56,491 adding 'MDAnalysis/analysis/helix_analysis.py' 2022-06-02T19:47:56,496 adding 'MDAnalysis/analysis/leaflet.py' 2022-06-02T19:47:56,501 adding 'MDAnalysis/analysis/lineardensity.py' 2022-06-02T19:47:56,507 adding 'MDAnalysis/analysis/msd.py' 2022-06-02T19:47:56,510 adding 'MDAnalysis/analysis/nucleicacids.py' 2022-06-02T19:47:56,515 adding 'MDAnalysis/analysis/nuclinfo.py' 2022-06-02T19:47:56,525 adding 'MDAnalysis/analysis/pca.py' 2022-06-02T19:47:56,530 adding 'MDAnalysis/analysis/polymer.py' 2022-06-02T19:47:56,554 adding 'MDAnalysis/analysis/psa.py' 2022-06-02T19:47:56,561 adding 'MDAnalysis/analysis/rdf.py' 2022-06-02T19:47:56,572 adding 'MDAnalysis/analysis/rms.py' 2022-06-02T19:47:56,584 adding 'MDAnalysis/analysis/waterdynamics.py' 2022-06-02T19:47:56,588 adding 'MDAnalysis/analysis/data/__init__.py' 2022-06-02T19:47:56,590 adding 'MDAnalysis/analysis/data/filenames.py' 2022-06-02T19:47:56,598 adding 'MDAnalysis/analysis/data/janin_ref_data.npy' 2022-06-02T19:47:56,611 adding 'MDAnalysis/analysis/data/rama_ref_data.npy' 2022-06-02T19:47:56,616 adding 'MDAnalysis/analysis/encore/__init__.py' 2022-06-02T19:47:56,619 adding 'MDAnalysis/analysis/encore/bootstrap.py' 2022-06-02T19:47:56,623 adding 'MDAnalysis/analysis/encore/confdistmatrix.py' 2022-06-02T19:47:56,627 adding 'MDAnalysis/analysis/encore/covariance.py' 2022-06-02T19:47:56,715 adding 'MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:47:56,733 adding 'MDAnalysis/analysis/encore/similarity.py' 2022-06-02T19:47:56,739 adding 'MDAnalysis/analysis/encore/utils.py' 2022-06-02T19:47:56,744 adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' 2022-06-02T19:47:56,749 adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' 2022-06-02T19:47:56,751 adding 'MDAnalysis/analysis/encore/clustering/__init__.py' 2022-06-02T19:47:57,014 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:47:57,028 adding 'MDAnalysis/analysis/encore/clustering/cluster.py' 2022-06-02T19:47:57,032 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' 2022-06-02T19:47:57,035 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' 2022-06-02T19:47:57,039 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' 2022-06-02T19:47:57,206 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:47:57,215 adding 'MDAnalysis/analysis/hbonds/__init__.py' 2022-06-02T19:47:57,218 adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' 2022-06-02T19:47:57,223 adding 'MDAnalysis/analysis/hole2/__init__.py' 2022-06-02T19:47:57,237 adding 'MDAnalysis/analysis/hole2/hole.py' 2022-06-02T19:47:57,241 adding 'MDAnalysis/analysis/hole2/templates.py' 2022-06-02T19:47:57,247 adding 'MDAnalysis/analysis/hole2/utils.py' 2022-06-02T19:47:57,251 adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' 2022-06-02T19:47:57,260 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' 2022-06-02T19:47:57,268 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' 2022-06-02T19:47:57,290 adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' 2022-06-02T19:47:57,295 adding 'MDAnalysis/analysis/legacy/__init__.py' 2022-06-02T19:47:57,304 adding 'MDAnalysis/analysis/legacy/x3dna.py' 2022-06-02T19:47:57,310 adding 'MDAnalysis/auxiliary/XVG.py' 2022-06-02T19:47:57,316 adding 'MDAnalysis/auxiliary/__init__.py' 2022-06-02T19:47:57,327 adding 'MDAnalysis/auxiliary/base.py' 2022-06-02T19:47:57,330 adding 'MDAnalysis/auxiliary/core.py' 2022-06-02T19:47:57,334 adding 'MDAnalysis/converters/OpenMM.py' 2022-06-02T19:47:57,338 adding 'MDAnalysis/converters/OpenMMParser.py' 2022-06-02T19:47:57,343 adding 'MDAnalysis/converters/ParmEd.py' 2022-06-02T19:47:57,347 adding 'MDAnalysis/converters/ParmEdParser.py' 2022-06-02T19:47:57,359 adding 'MDAnalysis/converters/RDKit.py' 2022-06-02T19:47:57,364 adding 'MDAnalysis/converters/RDKitParser.py' 2022-06-02T19:47:57,367 adding 'MDAnalysis/converters/__init__.py' 2022-06-02T19:47:57,371 adding 'MDAnalysis/coordinates/CRD.py' 2022-06-02T19:47:57,377 adding 'MDAnalysis/coordinates/DCD.py' 2022-06-02T19:47:57,381 adding 'MDAnalysis/coordinates/DLPoly.py' 2022-06-02T19:47:57,384 adding 'MDAnalysis/coordinates/DMS.py' 2022-06-02T19:47:57,389 adding 'MDAnalysis/coordinates/FHIAIMS.py' 2022-06-02T19:47:57,392 adding 'MDAnalysis/coordinates/GMS.py' 2022-06-02T19:47:57,398 adding 'MDAnalysis/coordinates/GRO.py' 2022-06-02T19:47:57,402 adding 'MDAnalysis/coordinates/GSD.py' 2022-06-02T19:47:57,420 adding 'MDAnalysis/coordinates/H5MD.py' 2022-06-02T19:47:57,424 adding 'MDAnalysis/coordinates/INPCRD.py' 2022-06-02T19:47:57,431 adding 'MDAnalysis/coordinates/LAMMPS.py' 2022-06-02T19:47:57,435 adding 'MDAnalysis/coordinates/MMTF.py' 2022-06-02T19:47:57,439 adding 'MDAnalysis/coordinates/MOL2.py' 2022-06-02T19:47:57,443 adding 'MDAnalysis/coordinates/NAMDBIN.py' 2022-06-02T19:47:57,459 adding 'MDAnalysis/coordinates/PDB.py' 2022-06-02T19:47:57,465 adding 'MDAnalysis/coordinates/PDBQT.py' 2022-06-02T19:47:57,470 adding 'MDAnalysis/coordinates/PQR.py' 2022-06-02T19:47:57,473 adding 'MDAnalysis/coordinates/ParmEd.py' 2022-06-02T19:47:57,487 adding 'MDAnalysis/coordinates/TRJ.py' 2022-06-02T19:47:57,492 adding 'MDAnalysis/coordinates/TRR.py' 2022-06-02T19:47:57,498 adding 'MDAnalysis/coordinates/TRZ.py' 2022-06-02T19:47:57,501 adding 'MDAnalysis/coordinates/TXYZ.py' 2022-06-02T19:47:57,506 adding 'MDAnalysis/coordinates/XDR.py' 2022-06-02T19:47:57,509 adding 'MDAnalysis/coordinates/XTC.py' 2022-06-02T19:47:57,515 adding 'MDAnalysis/coordinates/XYZ.py' 2022-06-02T19:47:57,526 adding 'MDAnalysis/coordinates/__init__.py' 2022-06-02T19:47:57,549 adding 'MDAnalysis/coordinates/base.py' 2022-06-02T19:47:57,559 adding 'MDAnalysis/coordinates/chain.py' 2022-06-02T19:47:57,565 adding 'MDAnalysis/coordinates/chemfiles.py' 2022-06-02T19:47:57,568 adding 'MDAnalysis/coordinates/core.py' 2022-06-02T19:47:57,575 adding 'MDAnalysis/coordinates/memory.py' 2022-06-02T19:47:57,578 adding 'MDAnalysis/coordinates/null.py' 2022-06-02T19:47:57,582 adding 'MDAnalysis/core/__init__.py' 2022-06-02T19:47:57,586 adding 'MDAnalysis/core/_get_readers.py' 2022-06-02T19:47:57,589 adding 'MDAnalysis/core/accessors.py' 2022-06-02T19:47:57,640 adding 'MDAnalysis/core/groups.py' 2022-06-02T19:47:57,659 adding 'MDAnalysis/core/selection.py' 2022-06-02T19:47:57,665 adding 'MDAnalysis/core/topology.py' 2022-06-02T19:47:57,689 adding 'MDAnalysis/core/topologyattrs.py' 2022-06-02T19:47:57,699 adding 'MDAnalysis/core/topologyobjects.py' 2022-06-02T19:47:57,718 adding 'MDAnalysis/core/universe.py' 2022-06-02T19:47:57,723 adding 'MDAnalysis/lib/NeighborSearch.py' 2022-06-02T19:47:57,725 adding 'MDAnalysis/lib/__init__.py' 2022-06-02T19:47:58,389 adding 'MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:47:59,268 adding 'MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:47:59,438 adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:48:00,239 adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:48:00,422 adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:48:00,433 adding 'MDAnalysis/lib/correlations.py' 2022-06-02T19:48:00,445 adding 'MDAnalysis/lib/distances.py' 2022-06-02T19:48:00,452 adding 'MDAnalysis/lib/log.py' 2022-06-02T19:48:00,457 adding 'MDAnalysis/lib/mdamath.py' 2022-06-02T19:48:01,267 adding 'MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:48:01,305 adding 'MDAnalysis/lib/picklable_file_io.py' 2022-06-02T19:48:01,309 adding 'MDAnalysis/lib/pkdtree.py' 2022-06-02T19:48:01,493 adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:48:01,517 adding 'MDAnalysis/lib/transformations.py' 2022-06-02T19:48:01,545 adding 'MDAnalysis/lib/util.py' 2022-06-02T19:48:01,549 adding 'MDAnalysis/lib/formats/__init__.py' 2022-06-02T19:48:02,051 adding 'MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:48:03,057 adding 'MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:48:04,093 adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so' 2022-06-02T19:48:04,138 adding 'MDAnalysis/selections/__init__.py' 2022-06-02T19:48:04,142 adding 'MDAnalysis/selections/base.py' 2022-06-02T19:48:04,146 adding 'MDAnalysis/selections/charmm.py' 2022-06-02T19:48:04,149 adding 'MDAnalysis/selections/gromacs.py' 2022-06-02T19:48:04,151 adding 'MDAnalysis/selections/jmol.py' 2022-06-02T19:48:04,154 adding 'MDAnalysis/selections/pymol.py' 2022-06-02T19:48:04,157 adding 'MDAnalysis/selections/vmd.py' 2022-06-02T19:48:04,161 adding 'MDAnalysis/tests/__init__.py' 2022-06-02T19:48:04,164 adding 'MDAnalysis/tests/datafiles.py' 2022-06-02T19:48:04,168 adding 'MDAnalysis/topology/CRDParser.py' 2022-06-02T19:48:04,171 adding 'MDAnalysis/topology/DLPolyParser.py' 2022-06-02T19:48:04,175 adding 'MDAnalysis/topology/DMSParser.py' 2022-06-02T19:48:04,178 adding 'MDAnalysis/topology/ExtendedPDBParser.py' 2022-06-02T19:48:04,181 adding 'MDAnalysis/topology/FHIAIMSParser.py' 2022-06-02T19:48:04,184 adding 'MDAnalysis/topology/GMSParser.py' 2022-06-02T19:48:04,188 adding 'MDAnalysis/topology/GROParser.py' 2022-06-02T19:48:04,191 adding 'MDAnalysis/topology/GSDParser.py' 2022-06-02T19:48:04,195 adding 'MDAnalysis/topology/HoomdXMLParser.py' 2022-06-02T19:48:04,202 adding 'MDAnalysis/topology/ITPParser.py' 2022-06-02T19:48:04,209 adding 'MDAnalysis/topology/LAMMPSParser.py' 2022-06-02T19:48:04,213 adding 'MDAnalysis/topology/MMTFParser.py' 2022-06-02T19:48:04,218 adding 'MDAnalysis/topology/MOL2Parser.py' 2022-06-02T19:48:04,221 adding 'MDAnalysis/topology/MinimalParser.py' 2022-06-02T19:48:04,226 adding 'MDAnalysis/topology/PDBParser.py' 2022-06-02T19:48:04,230 adding 'MDAnalysis/topology/PDBQTParser.py' 2022-06-02T19:48:04,234 adding 'MDAnalysis/topology/PQRParser.py' 2022-06-02T19:48:04,238 adding 'MDAnalysis/topology/PSFParser.py' 2022-06-02T19:48:04,241 adding 'MDAnalysis/topology/ParmEdParser.py' 2022-06-02T19:48:04,248 adding 'MDAnalysis/topology/TOPParser.py' 2022-06-02T19:48:04,253 adding 'MDAnalysis/topology/TPRParser.py' 2022-06-02T19:48:04,256 adding 'MDAnalysis/topology/TXYZParser.py' 2022-06-02T19:48:04,259 adding 'MDAnalysis/topology/XYZParser.py' 2022-06-02T19:48:04,264 adding 'MDAnalysis/topology/__init__.py' 2022-06-02T19:48:04,269 adding 'MDAnalysis/topology/base.py' 2022-06-02T19:48:04,272 adding 'MDAnalysis/topology/core.py' 2022-06-02T19:48:04,278 adding 'MDAnalysis/topology/guessers.py' 2022-06-02T19:48:04,283 adding 'MDAnalysis/topology/tables.py' 2022-06-02T19:48:04,287 adding 'MDAnalysis/topology/tpr/__init__.py' 2022-06-02T19:48:04,290 adding 'MDAnalysis/topology/tpr/obj.py' 2022-06-02T19:48:04,294 adding 'MDAnalysis/topology/tpr/setting.py' 2022-06-02T19:48:04,303 adding 'MDAnalysis/topology/tpr/utils.py' 2022-06-02T19:48:04,307 adding 'MDAnalysis/transformations/__init__.py' 2022-06-02T19:48:04,311 adding 'MDAnalysis/transformations/base.py' 2022-06-02T19:48:04,314 adding 'MDAnalysis/transformations/boxdimensions.py' 2022-06-02T19:48:04,318 adding 'MDAnalysis/transformations/fit.py' 2022-06-02T19:48:04,322 adding 'MDAnalysis/transformations/positionaveraging.py' 2022-06-02T19:48:04,325 adding 'MDAnalysis/transformations/rotate.py' 2022-06-02T19:48:04,329 adding 'MDAnalysis/transformations/translate.py' 2022-06-02T19:48:04,333 adding 'MDAnalysis/transformations/wrap.py' 2022-06-02T19:48:04,336 adding 'MDAnalysis/visualization/__init__.py' 2022-06-02T19:48:04,342 adding 'MDAnalysis/visualization/streamlines.py' 2022-06-02T19:48:04,350 adding 'MDAnalysis/visualization/streamlines_3D.py' 2022-06-02T19:48:04,356 adding 'MDAnalysis-2.2.0.dist-info/AUTHORS' 2022-06-02T19:48:04,364 adding 'MDAnalysis-2.2.0.dist-info/LICENSE' 2022-06-02T19:48:04,367 adding 'MDAnalysis-2.2.0.dist-info/METADATA' 2022-06-02T19:48:04,369 adding 'MDAnalysis-2.2.0.dist-info/WHEEL' 2022-06-02T19:48:04,370 adding 'MDAnalysis-2.2.0.dist-info/top_level.txt' 2022-06-02T19:48:04,378 adding 'MDAnalysis-2.2.0.dist-info/RECORD' 2022-06-02T19:48:04,601 removing build/bdist.linux-armv7l/wheel 2022-06-02T19:48:05,126 Building wheel for mdanalysis (pyproject.toml): finished with status 'done' 2022-06-02T19:48:05,441 Created wheel for mdanalysis: filename=MDAnalysis-2.2.0-cp39-cp39-linux_armv7l.whl size=5903571 sha256=4d852c41177612532ba7f7ec2627465cdaa02e4f2d480c72586209ed68e9827f 2022-06-02T19:48:05,444 Stored in directory: /tmp/pip-ephem-wheel-cache-x4rsn4cl/wheels/26/96/b3/aedf2710b2d516482b15c908124c808659cb6368ee371c29b5 2022-06-02T19:48:05,489 Successfully built mdanalysis 2022-06-02T19:48:05,917 Removed build tracker: '/tmp/pip-build-tracker-9e2zji9q'