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https://files.pythonhosted.org/packages/a6/35/cf1c6a669eabb4e6b9c66e5f60214eef0d111c82dca16c265afd9a1f61e5/MDAnalysis-2.6.0-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,613 Found link https://files.pythonhosted.org/packages/b8/1b/12f34fc28e41c12d05f299012fed63cedf2d733057ca5ea7ef1854efb027/MDAnalysis-2.6.0.tar.gz (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9), version: 2.6.0 2023-08-29T02:48:32,613 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/d3/17/9f60da41a30036dce229edf049995eec74aa62713b0d9648ed5f9aec3bad/MDAnalysis-2.6.1-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,613 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/b3/e3/07df8ad49734110f5fde7698259ae1e9469b54f5e5f81f7a1ce217b61a5f/MDAnalysis-2.6.1-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,614 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/fe/0a/bf186c0bc8332962a4e9085eafc5dd7672289453bf49c8daba95523e1e94/MDAnalysis-2.6.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,614 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/90/c6/c2ec55f7ef4a7fe1120ded656bdc8cbac9172c242d440d0cf4e3aac956ca/MDAnalysis-2.6.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,614 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/23/48/8f3d9538d15909542fa6db82eff31fc29da0a11978dcb92dcb49c315e2f6/MDAnalysis-2.6.1-cp310-cp310-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,614 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/c5/03/259de57764f65bba1e380628a2db0c5b4983d7644a3a294e31bd3d346792/MDAnalysis-2.6.1-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,614 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/c1/34/7542d1f4ff58828d33500c4b7f93948131797a8fa193e1943090ef21157e/MDAnalysis-2.6.1-cp311-cp311-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,615 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/7b/c2/a7a75fa0aad84a812a79c75f043c2f866c3b976403516aebccc8bfac4df0/MDAnalysis-2.6.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,615 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/bf/5d/f07ae9f2294615f400bf49bd77efa0c0a44c653b50983cdf5e560f0e6da5/MDAnalysis-2.6.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,615 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/c4/09/f583d8a7cca23c493d89f85c4e82608c4ab20e47be9932c0ae508104d52d/MDAnalysis-2.6.1-cp311-cp311-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,615 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/90/72/8c70e522431b5ecefd01c6c652004836ff41310e901db9f4671604f2a59d/MDAnalysis-2.6.1-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,615 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/06/0b/61f82278421c83499ca33e31d59b033c9302e32f99b9bf5cb6aa9acf9e54/MDAnalysis-2.6.1-cp39-cp39-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,616 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/f0/36/8d4a1d03188661563696e0c666a9bb3d1907c0acae4e518f495143380f8e/MDAnalysis-2.6.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,616 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/a7/48/c66fa9381aa89165f6d732f71103f39bfd42f8b6bfc7c901b9973b435344/MDAnalysis-2.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,616 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/cd/f4/9ad2217466d523c3285bae9610041e407c8d5ad7582b2783a553a38d07d6/MDAnalysis-2.6.1-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,617 Found link https://files.pythonhosted.org/packages/c0/2a/ac39b12836ef0d27937b4765d8e17b09b94f7de9092d4cf657dd336f2663/MDAnalysis-2.6.1.tar.gz (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.9), version: 2.6.1 2023-08-29T02:48:32,617 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdanalysis/ 2023-08-29T02:48:32,617 Getting page https://www.piwheels.org/simple/mdanalysis/ 2023-08-29T02:48:32,618 Found index url https://www.piwheels.org/simple/ 2023-08-29T02:48:32,777 Fetched page https://www.piwheels.org/simple/mdanalysis/ as text/html 2023-08-29T02:48:32,808 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.6.0-cp39-cp39-linux_armv7l.whl#sha256=85cf13c9a14a89cd6241fa6ce79a1f99fb90a3fd801d521f9f31f0ba54b6ff8a (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,808 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.6.0-cp39-cp39-linux_armv6l.whl#sha256=85cf13c9a14a89cd6241fa6ce79a1f99fb90a3fd801d521f9f31f0ba54b6ff8a (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,808 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.5.0-cp39-cp39-linux_armv7l.whl#sha256=332587d7301732247bb5add53a9b3eff4921e3c9b5f24b22f5067a668ddc4249 (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,809 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.5.0-cp39-cp39-linux_armv6l.whl#sha256=332587d7301732247bb5add53a9b3eff4921e3c9b5f24b22f5067a668ddc4249 (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.9) 2023-08-29T02:48:32,809 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.4.3-cp39-cp39-linux_armv7l.whl#sha256=385768a1cbe3cb8f6dabd63687b4e5ed03a5bb6c39ab90c5b75914881d468334 (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-08-29T02:48:32,809 Skipping link: No binaries permitted for mdanalysis: 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2023-08-29T02:48:32,814 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) 2023-08-29T02:48:32,815 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=1214ca3490e50243b48350c6c6a2c89b77cce8f1cd72f6d2549860b3db1ad84c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2023-08-29T02:48:32,815 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/) 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.1-cp37-cp37m-linux_armv6l.whl#sha256=82dd02ba237b4261c0f0d1f180ee08cda6cd1c25871e12db138518ab9f8ca8a6 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,821 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.1-cp37-cp37m-linux_armv7l.whl#sha256=82dd02ba237b4261c0f0d1f180ee08cda6cd1c25871e12db138518ab9f8ca8a6 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,821 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp34-cp34m-linux_armv7l.whl#sha256=2182ab1095b6fb7758816fb8041d325e39216149dd9cc19f98b2394392a14f1b (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,821 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp34-cp34m-linux_armv6l.whl#sha256=2182ab1095b6fb7758816fb8041d325e39216149dd9cc19f98b2394392a14f1b (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,821 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp35-cp35m-linux_armv6l.whl#sha256=426923348f9332d0762be3c94068ab6f54e143815453ae85d2a749e77e4226f7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,821 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp35-cp35m-linux_armv7l.whl#sha256=426923348f9332d0762be3c94068ab6f54e143815453ae85d2a749e77e4226f7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,822 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp37-cp37m-linux_armv7l.whl#sha256=12656c0ac065200b557f80654ef49efaf3e7605ed9abdb94875f64143616f41d (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,822 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.19.0-cp37-cp37m-linux_armv6l.whl#sha256=12656c0ac065200b557f80654ef49efaf3e7605ed9abdb94875f64143616f41d (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,822 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp34-cp34m-linux_armv7l.whl#sha256=9ed92944cd4b3322d05b9a4bb840fe590ed3be07609a93ffb09fe1f760ac363d (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,822 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp34-cp34m-linux_armv6l.whl#sha256=9ed92944cd4b3322d05b9a4bb840fe590ed3be07609a93ffb09fe1f760ac363d (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,822 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp35-cp35m-linux_armv7l.whl#sha256=66b3e7f35c28b424a6ad19307554c223ebc24916dddb557dbd08762989c32119 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,823 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp35-cp35m-linux_armv6l.whl#sha256=66b3e7f35c28b424a6ad19307554c223ebc24916dddb557dbd08762989c32119 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,823 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp37-cp37m-linux_armv6l.whl#sha256=07e291f5c3ee08d16b280c629411107ae1984f33458036e3418429e5f1a33092 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,823 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp37-cp37m-linux_armv7l.whl#sha256=07e291f5c3ee08d16b280c629411107ae1984f33458036e3418429e5f1a33092 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,823 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp37-cp37m-linux_armv7l.whl#sha256=bff2b2b18becae8ee1095f65c6e0d35f33fbc31544d3a12e9ab41bcdb6a775ce (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,823 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp37-cp37m-linux_armv6l.whl#sha256=bff2b2b18becae8ee1095f65c6e0d35f33fbc31544d3a12e9ab41bcdb6a775ce (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,824 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp34-cp34m-linux_armv6l.whl#sha256=ca0488c00e0be959cac05340ae1deb148c2769996e5abb346ad3a7487c2193d1 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,824 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp34-cp34m-linux_armv7l.whl#sha256=ca0488c00e0be959cac05340ae1deb148c2769996e5abb346ad3a7487c2193d1 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,824 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp35-cp35m-linux_armv6l.whl#sha256=58492c63068e648dfb1879b19f1fa55e6e3b9589ee9141eda53c4aed5a915136 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,824 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp35-cp35m-linux_armv7l.whl#sha256=58492c63068e648dfb1879b19f1fa55e6e3b9589ee9141eda53c4aed5a915136 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,824 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp35-cp35m-linux_armv6l.whl#sha256=28e395835220893e8a10d101072b742e6401a4376ddfacc41e30572d8aa6ed65 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,825 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp35-cp35m-linux_armv7l.whl#sha256=28e395835220893e8a10d101072b742e6401a4376ddfacc41e30572d8aa6ed65 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,825 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp34-cp34m-linux_armv6l.whl#sha256=e959b452e988fe4a9b8459143d6a64eef168bc3b9355a04b20ba20c4bb1bf601 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,825 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp34-cp34m-linux_armv7l.whl#sha256=e959b452e988fe4a9b8459143d6a64eef168bc3b9355a04b20ba20c4bb1bf601 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,825 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp34-cp34m-linux_armv6l.whl#sha256=985988f3d88079fe20f14ddee546fbb7b13e2a70dbeb4ac10c0f38f45afa7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,825 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp34-cp34m-linux_armv7l.whl#sha256=985988f3d88079fe20f14ddee546fbb7b13e2a70dbeb4ac10c0f38f45afa7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,826 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp35-cp35m-linux_armv7l.whl#sha256=933bf37f65e3ae59c832a6798365a3da99432510fcfc802e2d6eaa48db3a7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,826 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp35-cp35m-linux_armv6l.whl#sha256=933bf37f65e3ae59c832a6798365a3da99432510fcfc802e2d6eaa48db3a7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,826 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp34-cp34m-linux_armv6l.whl#sha256=34198e0f9e509df1779c2255812cee0f720dc8e989c7d4b7196337f75f1ef51b (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,826 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp34-cp34m-linux_armv7l.whl#sha256=34198e0f9e509df1779c2255812cee0f720dc8e989c7d4b7196337f75f1ef51b (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,826 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp35-cp35m-linux_armv7l.whl#sha256=032867bf17eecd5fd249607198ad5c191fac901f2856d5a485ffc53a8eb687d4 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,827 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp35-cp35m-linux_armv6l.whl#sha256=032867bf17eecd5fd249607198ad5c191fac901f2856d5a485ffc53a8eb687d4 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,827 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp35-cp35m-linux_armv7l.whl#sha256=04685acd7ab3d9f580c6dccdc18dfa33d89ea596521eede98bef2ec3f8f58af7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,827 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp35-cp35m-linux_armv6l.whl#sha256=04685acd7ab3d9f580c6dccdc18dfa33d89ea596521eede98bef2ec3f8f58af7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,827 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp34-cp34m-linux_armv6l.whl#sha256=30c2bb9cf26e969dbdc8978bd4710e9e8a42ee42ed7c9ad506c63a0855448307 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,827 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp34-cp34m-linux_armv7l.whl#sha256=30c2bb9cf26e969dbdc8978bd4710e9e8a42ee42ed7c9ad506c63a0855448307 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,827 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp34-cp34m-linux_armv6l.whl#sha256=527918d821e76043cda119ee29aa26b835f8f85251d560d47616e9147b5a1539 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,828 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp34-cp34m-linux_armv7l.whl#sha256=527918d821e76043cda119ee29aa26b835f8f85251d560d47616e9147b5a1539 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,828 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp35-cp35m-linux_armv6l.whl#sha256=b9d6e5734efb33b9383183904d491de8ef28aeeac7bbfdd617d48084126af113 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,828 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp35-cp35m-linux_armv7l.whl#sha256=46ca86446af4c56b5805a1cb36dd77ac64d009abb5500878ea4fa26320c7ba43 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,829 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/) 2023-08-29T02:48:32,829 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/) 2023-08-29T02:48:32,829 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/) 2023-08-29T02:48:32,829 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/) 2023-08-29T02:48:32,830 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp37-cp37m-linux_armv6l.whl#sha256=a073eda71f157be82bd9b81ac12793e63834dde1ac9b63ca704668a88b025c1e (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,830 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp35-cp35m-linux_armv7l.whl#sha256=47de147e5ee68a99b75107632aaa1e3bf84b4fa1f5bd7a456c1537266d437fbb (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,830 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/) 2023-08-29T02:48:32,830 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/) 2023-08-29T02:48:32,830 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/) 2023-08-29T02:48:32,831 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/) 2023-08-29T02:48:32,831 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp35-cp35m-linux_armv7l.whl#sha256=28a9bbed8fd84f6ebdf4efb48ef9e2435715169ef7a558ad7f11a33232e83815 (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,831 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp34-cp34m-linux_armv6l.whl#sha256=6d813f8dee5bde52fe344b851079bfaab34030f253869d7098ee33929566e36a (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,831 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp34-cp34m-linux_armv7l.whl#sha256=6d813f8dee5bde52fe344b851079bfaab34030f253869d7098ee33929566e36a (from https://www.piwheels.org/simple/mdanalysis/) 2023-08-29T02:48:32,831 Skipping link: not a file: https://www.piwheels.org/simple/mdanalysis/ 2023-08-29T02:48:32,832 Skipping link: not a file: https://pypi.org/simple/mdanalysis/ 2023-08-29T02:48:32,854 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates 2023-08-29T02:48:32,870 Collecting mdanalysis==2.6.1 2023-08-29T02:48:32,873 Created temporary directory: /tmp/pip-unpack-1pueht_q 2023-08-29T02:48:33,021 Downloading MDAnalysis-2.6.1.tar.gz (4.2 MB) 2023-08-29T02:48:35,740 Added mdanalysis==2.6.1 from https://files.pythonhosted.org/packages/c0/2a/ac39b12836ef0d27937b4765d8e17b09b94f7de9092d4cf657dd336f2663/MDAnalysis-2.6.1.tar.gz to build tracker '/tmp/pip-build-tracker-9kxkbgp7' 2023-08-29T02:48:35,762 Created temporary directory: /tmp/pip-build-env-5tvu3e23 2023-08-29T02:48:35,774 Installing build dependencies: started 2023-08-29T02:48:35,775 Running command pip subprocess to install build dependencies 2023-08-29T02:48:37,023 Using pip 23.1.2 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2023-08-29T02:48:37,421 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-08-29T02:48:37,422 Ignoring numpy: markers 'python_version == "3.10" and platform_python_implementation != "PyPy"' don't match your environment 2023-08-29T02:48:37,423 Ignoring numpy: markers 'python_version == "3.11" and platform_python_implementation != "PyPy"' don't match your environment 2023-08-29T02:48:37,424 Ignoring numpy: markers 'python_version >= "3.12"' don't match your environment 2023-08-29T02:48:39,257 Collecting Cython>=0.28 2023-08-29T02:48:40,022 Using cached https://www.piwheels.org/simple/cython/Cython-3.0.2-cp39-cp39-linux_armv7l.whl (10.7 MB) 2023-08-29T02:48:40,462 Collecting packaging 2023-08-29T02:48:40,479 Using cached https://www.piwheels.org/simple/packaging/packaging-23.1-py3-none-any.whl (48 kB) 2023-08-29T02:48:41,728 Collecting numpy==1.22.3 2023-08-29T02:48:41,743 Downloading https://www.piwheels.org/simple/numpy/numpy-1.22.3-cp39-cp39-linux_armv7l.whl (12.9 MB) 2023-08-29T02:48:42,694 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.9/12.9 MB 12.4 MB/s eta 0:00:00 2023-08-29T02:48:44,405 Collecting setuptools 2023-08-29T02:48:44,470 Using cached https://www.piwheels.org/simple/setuptools/setuptools-68.1.2-py3-none-any.whl (805 kB) 2023-08-29T02:48:44,725 Collecting wheel 2023-08-29T02:48:44,742 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-08-29T02:48:46,624 Installing collected packages: wheel, setuptools, packaging, numpy, Cython 2023-08-29T02:48:46,846 Creating /tmp/pip-build-env-5tvu3e23/overlay/bin 2023-08-29T02:48:46,849 changing mode of /tmp/pip-build-env-5tvu3e23/overlay/bin/wheel to 755 2023-08-29T02:48:57,057 changing mode of /tmp/pip-build-env-5tvu3e23/overlay/bin/f2py to 755 2023-08-29T02:48:57,060 changing mode of /tmp/pip-build-env-5tvu3e23/overlay/bin/f2py3 to 755 2023-08-29T02:48:57,062 changing mode of /tmp/pip-build-env-5tvu3e23/overlay/bin/f2py3.9 to 755 2023-08-29T02:49:00,645 changing mode of /tmp/pip-build-env-5tvu3e23/overlay/bin/cygdb to 755 2023-08-29T02:49:00,647 changing mode of /tmp/pip-build-env-5tvu3e23/overlay/bin/cython to 755 2023-08-29T02:49:00,649 changing mode of /tmp/pip-build-env-5tvu3e23/overlay/bin/cythonize to 755 2023-08-29T02:49:00,673 Successfully installed Cython-3.0.2 numpy-1.22.3 packaging-23.1 setuptools-68.1.2 wheel-0.41.2 2023-08-29T02:49:00,686 [notice] A new release of pip is available: 23.1.2 -> 23.2.1 2023-08-29T02:49:00,686 [notice] To update, run: python3 -m pip install --upgrade pip 2023-08-29T02:49:01,081 Installing build dependencies: finished with status 'done' 2023-08-29T02:49:01,091 Getting requirements to build wheel: started 2023-08-29T02:49:01,092 Running command Getting requirements to build wheel 2023-08-29T02:49:33,548 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-08-29T02:49:33,549 Will attempt to use Cython. 2023-08-29T02:49:33,549 Compiling MDAnalysis/lib/formats/libdcd.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,549 Compiling MDAnalysis/lib/c_distances.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,549 Compiling MDAnalysis/lib/c_distances_openmp.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,550 Compiling MDAnalysis/lib/qcprot.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,550 Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,550 Compiling MDAnalysis/lib/formats/cython_util.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,550 Compiling MDAnalysis/analysis/encore/cutils.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,550 Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,550 Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-08-29T02:49:33,550 Compiling MDAnalysis/lib/_cutil.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-08-29T02:49:33,551 Compiling MDAnalysis/lib/_augment.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-08-29T02:49:33,551 Compiling MDAnalysis/lib/nsgrid.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-08-29T02:49:33,551 Compiling MDAnalysis/coordinates/timestep.pyx because it depends on /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/__init__.pxd. 2023-08-29T02:49:33,551 [ 1/13] Cythonizing MDAnalysis/lib/_augment.pyx 2023-08-29T02:49:33,551 [ 2/13] Cythonizing MDAnalysis/lib/_cutil.pyx 2023-08-29T02:49:33,551 [ 3/13] Cythonizing MDAnalysis/lib/nsgrid.pyx 2023-08-29T02:49:33,551 [ 4/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx 2023-08-29T02:49:33,552 [ 5/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx 2023-08-29T02:49:33,552 [ 6/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx 2023-08-29T02:49:33,552 [ 7/13] Cythonizing MDAnalysis/coordinates/timestep.pyx 2023-08-29T02:49:33,552 [ 8/13] Cythonizing MDAnalysis/lib/c_distances.pyx 2023-08-29T02:49:33,552 [ 9/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx 2023-08-29T02:49:33,552 [10/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx 2023-08-29T02:49:33,552 [11/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx 2023-08-29T02:49:33,553 [12/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx 2023-08-29T02:49:33,553 [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx 2023-08-29T02:49:34,427 Getting requirements to build wheel: finished with status 'done' 2023-08-29T02:49:34,439 Created temporary directory: /tmp/pip-modern-metadata-f4z3ux3f 2023-08-29T02:49:34,442 Preparing metadata (pyproject.toml): started 2023-08-29T02:49:34,443 Running command Preparing metadata (pyproject.toml) 2023-08-29T02:49:36,901 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-08-29T02:49:36,902 Will attempt to use Cython. 2023-08-29T02:49:37,027 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:80: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-08-29T02:49:37,027 corresp(dist, value, root_dir) 2023-08-29T02:49:37,301 running dist_info 2023-08-29T02:49:37,308 creating /tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis.egg-info 2023-08-29T02:49:37,313 writing /tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis.egg-info/PKG-INFO 2023-08-29T02:49:37,317 writing dependency_links to /tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis.egg-info/dependency_links.txt 2023-08-29T02:49:37,320 writing requirements to /tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis.egg-info/requires.txt 2023-08-29T02:49:37,321 writing top-level names to /tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis.egg-info/top_level.txt 2023-08-29T02:49:37,322 writing manifest file '/tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis.egg-info/SOURCES.txt' 2023-08-29T02:49:37,363 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,363 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,363 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,364 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,364 dependency 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included in the manifest: the path must be relative 2023-08-29T02:49:37,371 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,371 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,372 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,372 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,372 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,372 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,372 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,372 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,372 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,372 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,373 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,373 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,373 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,373 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,373 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,373 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,373 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,373 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,374 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,374 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,374 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:37,381 reading manifest file '/tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis.egg-info/SOURCES.txt' 2023-08-29T02:49:37,383 reading manifest template 'MANIFEST.in' 2023-08-29T02:49:37,531 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2023-08-29T02:49:37,532 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-08-29T02:49:37,534 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2023-08-29T02:49:37,535 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2023-08-29T02:49:37,537 warning: no previously-included files matching '*~' found anywhere in distribution 2023-08-29T02:49:37,538 warning: no previously-included files matching '.git' found anywhere in distribution 2023-08-29T02:49:37,538 adding license file 'LICENSE' 2023-08-29T02:49:37,539 adding license file 'AUTHORS' 2023-08-29T02:49:37,556 writing manifest file '/tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis.egg-info/SOURCES.txt' 2023-08-29T02:49:37,558 creating '/tmp/pip-modern-metadata-f4z3ux3f/MDAnalysis-2.6.1.dist-info' 2023-08-29T02:49:37,784 Preparing metadata (pyproject.toml): finished with status 'done' 2023-08-29T02:49:37,793 Source in /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5 has version 2.6.1, which satisfies requirement mdanalysis==2.6.1 from https://files.pythonhosted.org/packages/c0/2a/ac39b12836ef0d27937b4765d8e17b09b94f7de9092d4cf657dd336f2663/MDAnalysis-2.6.1.tar.gz 2023-08-29T02:49:37,794 Removed mdanalysis==2.6.1 from https://files.pythonhosted.org/packages/c0/2a/ac39b12836ef0d27937b4765d8e17b09b94f7de9092d4cf657dd336f2663/MDAnalysis-2.6.1.tar.gz from build tracker '/tmp/pip-build-tracker-9kxkbgp7' 2023-08-29T02:49:37,804 Created temporary directory: /tmp/pip-unpack-1kbgijsh 2023-08-29T02:49:37,804 Building wheels for collected packages: mdanalysis 2023-08-29T02:49:37,808 Created temporary directory: /tmp/pip-wheel-15n27tuo 2023-08-29T02:49:37,808 Destination directory: /tmp/pip-wheel-15n27tuo 2023-08-29T02:49:37,810 Building wheel for mdanalysis (pyproject.toml): started 2023-08-29T02:49:37,811 Running command Building wheel for mdanalysis (pyproject.toml) 2023-08-29T02:49:40,176 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-08-29T02:49:40,177 Will attempt to use Cython. 2023-08-29T02:49:40,298 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:80: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-08-29T02:49:40,299 corresp(dist, value, root_dir) 2023-08-29T02:49:40,545 running bdist_wheel 2023-08-29T02:49:40,570 running build 2023-08-29T02:49:40,571 running build_py 2023-08-29T02:49:40,578 creating build 2023-08-29T02:49:40,578 creating build/lib.linux-armv7l-cpython-39 2023-08-29T02:49:40,579 creating build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-08-29T02:49:40,581 copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-08-29T02:49:40,583 copying MDAnalysis/due.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-08-29T02:49:40,585 copying MDAnalysis/authors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-08-29T02:49:40,587 copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-08-29T02:49:40,589 copying MDAnalysis/units.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-08-29T02:49:40,592 copying MDAnalysis/version.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-08-29T02:49:40,594 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-08-29T02:49:40,595 copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-08-29T02:49:40,597 copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-08-29T02:49:40,599 copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-08-29T02:49:40,601 copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-08-29T02:49:40,603 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-08-29T02:49:40,605 copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-08-29T02:49:40,607 copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-08-29T02:49:40,609 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-08-29T02:49:40,610 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-08-29T02:49:40,613 copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-08-29T02:49:40,615 copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-08-29T02:49:40,618 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-08-29T02:49:40,619 copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-08-29T02:49:40,622 copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-08-29T02:49:40,624 copying MDAnalysis/converters/RDKit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-08-29T02:49:40,627 copying MDAnalysis/converters/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-08-29T02:49:40,629 copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-08-29T02:49:40,632 copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-08-29T02:49:40,634 copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-08-29T02:49:40,637 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-08-29T02:49:40,638 copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-08-29T02:49:40,640 copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-08-29T02:49:40,642 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-08-29T02:49:40,643 copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-08-29T02:49:40,646 copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-08-29T02:49:40,648 copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-08-29T02:49:40,651 copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-08-29T02:49:40,654 copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-08-29T02:49:40,658 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,659 copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,661 copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,663 copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,666 copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,668 copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,670 copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,673 copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,674 copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,677 copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,679 copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,682 copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,684 copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,687 copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,690 copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,693 copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,696 copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,698 copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,700 copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,703 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,705 copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,707 copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,710 copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,712 copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,714 copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,717 copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,720 copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,722 copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,724 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,727 copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,730 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,732 copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,735 copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,738 copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:40,741 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,742 copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,745 copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,747 copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,751 copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,753 copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,756 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,759 copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,761 copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,764 copying MDAnalysis/analysis/msd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,767 copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,769 copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,772 copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,775 copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,778 copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,780 copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,782 copying MDAnalysis/analysis/atomicdistances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,785 copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,787 copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,790 copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,791 copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,796 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,798 copying MDAnalysis/analysis/bat.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,801 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,803 copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:49:40,808 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,809 copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,811 copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,813 copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,816 copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,819 copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,821 copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,823 copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,825 copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,828 copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,830 copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,833 copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,835 copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,837 copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,840 copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,842 copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,845 copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,847 copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,850 copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,853 copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,855 copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,857 copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,859 copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,861 copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,863 copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,866 copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,868 copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,870 copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,871 copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-08-29T02:49:40,874 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,875 copying MDAnalysis/lib/_distopia.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,877 copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,880 copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,882 copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,885 copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,888 copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,890 copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,892 copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,896 copying MDAnalysis/lib/correlations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,898 copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,901 copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:40,905 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,906 copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,909 copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,916 copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,918 copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,922 copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,926 copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,928 copying MDAnalysis/core/accessors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,931 copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,933 copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-08-29T02:49:40,937 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,938 copying MDAnalysis/transformations/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,940 copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,942 copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,944 copying MDAnalysis/transformations/nojump.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,946 copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,949 copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,951 copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,953 copying MDAnalysis/transformations/wrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,955 copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-08-29T02:49:40,958 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:40,959 copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:40,961 copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:40,965 copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:40,967 copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:40,970 copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:40,972 copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:40,975 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-08-29T02:49:40,976 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-08-29T02:49:40,979 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-08-29T02:49:40,982 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-08-29T02:49:40,984 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-08-29T02:49:40,988 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-08-29T02:49:40,989 copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-08-29T02:49:40,992 copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-08-29T02:49:40,994 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:49:40,995 copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:49:40,999 copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:49:41,002 copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:49:41,005 copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:49:41,007 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-08-29T02:49:41,009 copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-08-29T02:49:41,011 copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-08-29T02:49:41,013 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-08-29T02:49:41,014 copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-08-29T02:49:41,016 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-08-29T02:49:41,018 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:49:41,019 copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:49:41,021 copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:49:41,023 copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:49:41,026 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-08-29T02:49:41,027 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-08-29T02:49:41,030 copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-08-29T02:49:41,033 copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-08-29T02:49:41,035 copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-08-29T02:49:41,037 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-08-29T02:49:41,038 copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-08-29T02:49:41,040 copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-08-29T02:49:41,042 copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-08-29T02:49:41,045 copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-08-29T02:49:41,048 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,049 copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,050 running egg_info 2023-08-29T02:49:41,057 writing MDAnalysis.egg-info/PKG-INFO 2023-08-29T02:49:41,060 writing dependency_links to MDAnalysis.egg-info/dependency_links.txt 2023-08-29T02:49:41,062 writing requirements to MDAnalysis.egg-info/requires.txt 2023-08-29T02:49:41,063 writing top-level names to MDAnalysis.egg-info/top_level.txt 2023-08-29T02:49:41,087 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,087 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,087 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,088 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,088 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,088 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,089 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,089 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,089 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,089 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,089 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,089 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,089 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,090 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,090 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,090 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,090 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,090 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,090 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,090 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,091 dependency 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manifest: the path must be relative 2023-08-29T02:49:41,091 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,091 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,093 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,093 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,093 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,093 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,093 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,093 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,093 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,094 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,094 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,094 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,094 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,094 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,094 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,095 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,095 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,095 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,095 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,095 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,095 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,095 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,095 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,096 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,096 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,096 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,096 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,096 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,096 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,096 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,096 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,097 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,097 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,097 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,097 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,097 dependency /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,097 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,097 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,098 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,098 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,098 dependency /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2023-08-29T02:49:41,103 reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2023-08-29T02:49:41,115 reading manifest template 'MANIFEST.in' 2023-08-29T02:49:41,315 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2023-08-29T02:49:41,319 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-08-29T02:49:41,323 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2023-08-29T02:49:41,328 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2023-08-29T02:49:41,332 warning: no previously-included files matching '*~' found anywhere in distribution 2023-08-29T02:49:41,335 warning: no previously-included files matching '.git' found anywhere in distribution 2023-08-29T02:49:41,335 adding license file 'LICENSE' 2023-08-29T02:49:41,335 adding license file 'AUTHORS' 2023-08-29T02:49:41,363 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2023-08-29T02:49:41,367 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.clustering.include' is absent from the `packages` configuration. 2023-08-29T02:49:41,368 !! 2023-08-29T02:49:41,368 ******************************************************************************** 2023-08-29T02:49:41,368 ############################ 2023-08-29T02:49:41,368 # Package would be ignored # 2023-08-29T02:49:41,368 ############################ 2023-08-29T02:49:41,368 Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package[^1], 2023-08-29T02:49:41,368 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,369 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,369 package, please make sure that 'MDAnalysis.analysis.encore.clustering.include' is explicitly added 2023-08-29T02:49:41,369 to the `packages` configuration field. 2023-08-29T02:49:41,369 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,369 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,369 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,370 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,370 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,370 If you don't want 'MDAnalysis.analysis.encore.clustering.include' to be distributed and are 2023-08-29T02:49:41,370 already explicitly excluding 'MDAnalysis.analysis.encore.clustering.include' via 2023-08-29T02:49:41,370 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,370 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,371 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,371 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,371 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,371 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,372 even if it does not contain any `.py` files. 2023-08-29T02:49:41,372 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,372 directory, all directories are treated like packages. 2023-08-29T02:49:41,372 ******************************************************************************** 2023-08-29T02:49:41,372 !! 2023-08-29T02:49:41,372 check.warn(importable) 2023-08-29T02:49:41,372 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.clustering.src' is absent from the `packages` configuration. 2023-08-29T02:49:41,373 !! 2023-08-29T02:49:41,373 ******************************************************************************** 2023-08-29T02:49:41,373 ############################ 2023-08-29T02:49:41,373 # Package would be ignored # 2023-08-29T02:49:41,373 ############################ 2023-08-29T02:49:41,373 Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package[^1], 2023-08-29T02:49:41,373 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,374 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,374 package, please make sure that 'MDAnalysis.analysis.encore.clustering.src' is explicitly added 2023-08-29T02:49:41,374 to the `packages` configuration field. 2023-08-29T02:49:41,374 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,374 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,374 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,375 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,375 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,375 If you don't want 'MDAnalysis.analysis.encore.clustering.src' to be distributed and are 2023-08-29T02:49:41,375 already explicitly excluding 'MDAnalysis.analysis.encore.clustering.src' via 2023-08-29T02:49:41,375 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,376 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,376 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,376 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,376 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,376 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,377 even if it does not contain any `.py` files. 2023-08-29T02:49:41,377 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,377 directory, all directories are treated like packages. 2023-08-29T02:49:41,377 ******************************************************************************** 2023-08-29T02:49:41,377 !! 2023-08-29T02:49:41,377 check.warn(importable) 2023-08-29T02:49:41,377 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is absent from the `packages` configuration. 2023-08-29T02:49:41,377 !! 2023-08-29T02:49:41,378 ******************************************************************************** 2023-08-29T02:49:41,378 ############################ 2023-08-29T02:49:41,378 # Package would be ignored # 2023-08-29T02:49:41,378 ############################ 2023-08-29T02:49:41,378 Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package[^1], 2023-08-29T02:49:41,378 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,378 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,379 package, please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is explicitly added 2023-08-29T02:49:41,379 to the `packages` configuration field. 2023-08-29T02:49:41,379 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,379 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,379 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,379 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,380 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,380 If you don't want 'MDAnalysis.analysis.encore.dimensionality_reduction.include' to be distributed and are 2023-08-29T02:49:41,380 already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.include' via 2023-08-29T02:49:41,380 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,380 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,380 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,381 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,381 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,381 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,381 even if it does not contain any `.py` files. 2023-08-29T02:49:41,381 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,381 directory, all directories are treated like packages. 2023-08-29T02:49:41,382 ******************************************************************************** 2023-08-29T02:49:41,382 !! 2023-08-29T02:49:41,382 check.warn(importable) 2023-08-29T02:49:41,382 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is absent from the `packages` configuration. 2023-08-29T02:49:41,382 !! 2023-08-29T02:49:41,382 ******************************************************************************** 2023-08-29T02:49:41,382 ############################ 2023-08-29T02:49:41,383 # Package would be ignored # 2023-08-29T02:49:41,383 ############################ 2023-08-29T02:49:41,383 Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package[^1], 2023-08-29T02:49:41,383 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,383 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,383 package, please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is explicitly added 2023-08-29T02:49:41,383 to the `packages` configuration field. 2023-08-29T02:49:41,384 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,384 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,384 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,384 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,384 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,384 If you don't want 'MDAnalysis.analysis.encore.dimensionality_reduction.src' to be distributed and are 2023-08-29T02:49:41,385 already explicitly excluding 'MDAnalysis.analysis.encore.dimensionality_reduction.src' via 2023-08-29T02:49:41,385 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,385 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,385 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,385 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,385 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,386 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,386 even if it does not contain any `.py` files. 2023-08-29T02:49:41,386 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,386 directory, all directories are treated like packages. 2023-08-29T02:49:41,386 ******************************************************************************** 2023-08-29T02:49:41,386 !! 2023-08-29T02:49:41,386 check.warn(importable) 2023-08-29T02:49:41,387 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.formats.include' is absent from the `packages` configuration. 2023-08-29T02:49:41,387 !! 2023-08-29T02:49:41,387 ******************************************************************************** 2023-08-29T02:49:41,387 ############################ 2023-08-29T02:49:41,387 # Package would be ignored # 2023-08-29T02:49:41,387 ############################ 2023-08-29T02:49:41,387 Python recognizes 'MDAnalysis.lib.formats.include' as an importable package[^1], 2023-08-29T02:49:41,388 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,388 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,388 package, please make sure that 'MDAnalysis.lib.formats.include' is explicitly added 2023-08-29T02:49:41,388 to the `packages` configuration field. 2023-08-29T02:49:41,388 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,388 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,389 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,389 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,389 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,389 If you don't want 'MDAnalysis.lib.formats.include' to be distributed and are 2023-08-29T02:49:41,389 already explicitly excluding 'MDAnalysis.lib.formats.include' via 2023-08-29T02:49:41,389 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,390 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,390 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,390 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,390 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,391 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,391 even if it does not contain any `.py` files. 2023-08-29T02:49:41,391 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,391 directory, all directories are treated like packages. 2023-08-29T02:49:41,391 ******************************************************************************** 2023-08-29T02:49:41,391 !! 2023-08-29T02:49:41,391 check.warn(importable) 2023-08-29T02:49:41,391 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.formats.src' is absent from the `packages` configuration. 2023-08-29T02:49:41,392 !! 2023-08-29T02:49:41,392 ******************************************************************************** 2023-08-29T02:49:41,392 ############################ 2023-08-29T02:49:41,392 # Package would be ignored # 2023-08-29T02:49:41,392 ############################ 2023-08-29T02:49:41,392 Python recognizes 'MDAnalysis.lib.formats.src' as an importable package[^1], 2023-08-29T02:49:41,392 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,393 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,393 package, please make sure that 'MDAnalysis.lib.formats.src' is explicitly added 2023-08-29T02:49:41,393 to the `packages` configuration field. 2023-08-29T02:49:41,393 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,393 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,393 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,394 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,394 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,394 If you don't want 'MDAnalysis.lib.formats.src' to be distributed and are 2023-08-29T02:49:41,394 already explicitly excluding 'MDAnalysis.lib.formats.src' via 2023-08-29T02:49:41,394 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,394 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,395 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,395 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,396 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,396 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,396 even if it does not contain any `.py` files. 2023-08-29T02:49:41,396 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,397 directory, all directories are treated like packages. 2023-08-29T02:49:41,397 ******************************************************************************** 2023-08-29T02:49:41,397 !! 2023-08-29T02:49:41,397 check.warn(importable) 2023-08-29T02:49:41,397 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.include' is absent from the `packages` configuration. 2023-08-29T02:49:41,397 !! 2023-08-29T02:49:41,398 ******************************************************************************** 2023-08-29T02:49:41,398 ############################ 2023-08-29T02:49:41,398 # Package would be ignored # 2023-08-29T02:49:41,398 ############################ 2023-08-29T02:49:41,398 Python recognizes 'MDAnalysis.lib.include' as an importable package[^1], 2023-08-29T02:49:41,398 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,399 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,399 package, please make sure that 'MDAnalysis.lib.include' is explicitly added 2023-08-29T02:49:41,399 to the `packages` configuration field. 2023-08-29T02:49:41,399 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,399 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,399 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,400 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,400 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,400 If you don't want 'MDAnalysis.lib.include' to be distributed and are 2023-08-29T02:49:41,400 already explicitly excluding 'MDAnalysis.lib.include' via 2023-08-29T02:49:41,400 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,401 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,401 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,401 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,401 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,402 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,402 even if it does not contain any `.py` files. 2023-08-29T02:49:41,402 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,402 directory, all directories are treated like packages. 2023-08-29T02:49:41,402 ******************************************************************************** 2023-08-29T02:49:41,402 !! 2023-08-29T02:49:41,402 check.warn(importable) 2023-08-29T02:49:41,403 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.libmdanalysis' is absent from the `packages` configuration. 2023-08-29T02:49:41,403 !! 2023-08-29T02:49:41,403 ******************************************************************************** 2023-08-29T02:49:41,403 ############################ 2023-08-29T02:49:41,403 # Package would be ignored # 2023-08-29T02:49:41,403 ############################ 2023-08-29T02:49:41,403 Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package[^1], 2023-08-29T02:49:41,404 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,404 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,404 package, please make sure that 'MDAnalysis.lib.libmdanalysis' is explicitly added 2023-08-29T02:49:41,404 to the `packages` configuration field. 2023-08-29T02:49:41,404 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,404 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,405 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,405 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,405 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,405 If you don't want 'MDAnalysis.lib.libmdanalysis' to be distributed and are 2023-08-29T02:49:41,406 already explicitly excluding 'MDAnalysis.lib.libmdanalysis' via 2023-08-29T02:49:41,406 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,409 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,414 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,415 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,415 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,415 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,416 even if it does not contain any `.py` files. 2023-08-29T02:49:41,416 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,416 directory, all directories are treated like packages. 2023-08-29T02:49:41,416 ******************************************************************************** 2023-08-29T02:49:41,416 !! 2023-08-29T02:49:41,416 check.warn(importable) 2023-08-29T02:49:41,416 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'MDAnalysis.lib.src.transformations' is absent from the `packages` configuration. 2023-08-29T02:49:41,417 !! 2023-08-29T02:49:41,417 ******************************************************************************** 2023-08-29T02:49:41,417 ############################ 2023-08-29T02:49:41,417 # Package would be ignored # 2023-08-29T02:49:41,417 ############################ 2023-08-29T02:49:41,417 Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package[^1], 2023-08-29T02:49:41,417 but it is absent from setuptools' `packages` configuration. 2023-08-29T02:49:41,418 This leads to an ambiguous overall configuration. If you want to distribute this 2023-08-29T02:49:41,418 package, please make sure that 'MDAnalysis.lib.src.transformations' is explicitly added 2023-08-29T02:49:41,418 to the `packages` configuration field. 2023-08-29T02:49:41,418 Alternatively, you can also rely on setuptools' discovery methods 2023-08-29T02:49:41,418 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-08-29T02:49:41,418 instead of `find_packages(...)`/`find:`). 2023-08-29T02:49:41,419 You can read more about "package discovery" on setuptools documentation page: 2023-08-29T02:49:41,419 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-08-29T02:49:41,419 If you don't want 'MDAnalysis.lib.src.transformations' to be distributed and are 2023-08-29T02:49:41,419 already explicitly excluding 'MDAnalysis.lib.src.transformations' via 2023-08-29T02:49:41,419 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-08-29T02:49:41,420 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-08-29T02:49:41,420 combination with a more fine grained `package-data` configuration. 2023-08-29T02:49:41,420 You can read more about "package data files" on setuptools documentation page: 2023-08-29T02:49:41,420 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-08-29T02:49:41,421 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-08-29T02:49:41,421 even if it does not contain any `.py` files. 2023-08-29T02:49:41,421 On the other hand, currently there is no concept of package data 2023-08-29T02:49:41,421 directory, all directories are treated like packages. 2023-08-29T02:49:41,421 ******************************************************************************** 2023-08-29T02:49:41,421 !! 2023-08-29T02:49:41,421 check.warn(importable) 2023-08-29T02:49:41,422 copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-08-29T02:49:41,422 copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-08-29T02:49:41,422 copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:41,422 copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:41,422 copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:49:41,424 copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,454 copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,459 copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,491 copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,493 copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,495 copying MDAnalysis/lib/c_distances.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,521 copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,524 copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,534 copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,537 copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,560 copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,563 copying MDAnalysis/lib/qcprot.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,574 copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,576 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include 2023-08-29T02:49:41,578 copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include 2023-08-29T02:49:41,581 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis 2023-08-29T02:49:41,582 copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis 2023-08-29T02:49:41,584 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src 2023-08-29T02:49:41,584 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-08-29T02:49:41,585 copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-08-29T02:49:41,587 copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-08-29T02:49:41,589 copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-08-29T02:49:41,594 copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:41,605 copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:49:41,608 copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:49:41,620 copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:49:41,622 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-08-29T02:49:41,623 copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-08-29T02:49:41,625 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-08-29T02:49:41,626 copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-08-29T02:49:41,628 copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-08-29T02:49:41,642 copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-08-29T02:49:41,645 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include 2023-08-29T02:49:41,646 copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include 2023-08-29T02:49:41,648 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-08-29T02:49:41,649 copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-08-29T02:49:41,652 copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,679 copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,681 copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,683 copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,709 copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,712 copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,715 copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,740 copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,742 copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,745 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,746 copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,749 copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,752 copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,755 copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,757 copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,760 copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,762 copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,764 copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-08-29T02:49:41,766 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-08-29T02:49:41,767 copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-08-29T02:49:41,769 copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-08-29T02:49:41,773 copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-08-29T02:49:41,776 copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-08-29T02:49:41,778 copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-08-29T02:49:41,797 running build_ext 2023-08-29T02:49:41,800 building 'MDAnalysis.lib.formats.libdcd' extension 2023-08-29T02:49:41,801 creating build/temp.linux-armv7l-cpython-39 2023-08-29T02:49:41,801 creating build/temp.linux-armv7l-cpython-39/MDAnalysis 2023-08-29T02:49:41,802 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib 2023-08-29T02:49:41,803 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-08-29T02:49:41,804 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-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:49:42,205 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:49:42,205 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:49:42,206 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:49:42,206 from MDAnalysis/lib/formats/libdcd.c:1188: 2023-08-29T02:49:42,206 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:49:42,206 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:49:42,206 | ^~~~~~~ 2023-08-29T02:49:42,268 In file included from MDAnalysis/lib/formats/libdcd.c:1195: 2023-08-29T02:49:42,268 MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’: 2023-08-29T02:49:42,268 MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-08-29T02:49:42,269 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2023-08-29T02:49:42,269 | ^~ 2023-08-29T02:49:42,271 MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’: 2023-08-29T02:49:42,271 MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable] 2023-08-29T02:49:42,271 698 | struct tm *tmbuf; 2023-08-29T02:49:42,272 | ^~~~~ 2023-08-29T02:49:42,272 MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable] 2023-08-29T02:49:42,272 697 | time_t cur_time; 2023-08-29T02:49:42,272 | ^~~~~~~~ 2023-08-29T02:49:44,684 In file included from MDAnalysis/lib/formats/include/readdcd.h:25, 2023-08-29T02:49:44,685 from MDAnalysis/lib/formats/libdcd.c:1195: 2023-08-29T02:49:44,685 At top level: 2023-08-29T02:49:44,685 MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2023-08-29T02:49:44,686 96 | static void swap2_aligned(void *v, long ndata) { 2023-08-29T02:49:44,686 | ^~~~~~~~~~~~~ 2023-08-29T02:49:44,686 MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2023-08-29T02:49:44,686 32 | static void swap2_unaligned(void *v, long ndata) { 2023-08-29T02:49:44,686 | ^~~~~~~~~~~~~~~ 2023-08-29T02:49:44,686 In file included from MDAnalysis/lib/formats/libdcd.c:1194: 2023-08-29T02:49:44,686 MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2023-08-29T02:49:44,687 453 | static int fio_write_str(fio_fd fd, const char *str) { 2023-08-29T02:49:44,687 | ^~~~~~~~~~~~~ 2023-08-29T02:49:44,687 MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2023-08-29T02:49:44,687 449 | static int fio_read_int32(fio_fd fd, int *i) { 2023-08-29T02:49:44,687 | ^~~~~~~~~~~~~~ 2023-08-29T02:50:36,565 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:50:36,787 building 'MDAnalysis.lib.c_distances' extension 2023-08-29T02:50:36,788 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:50:37,161 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:50:37,161 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:50:37,161 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:50:37,161 from MDAnalysis/lib/c_distances.c:1188: 2023-08-29T02:50:37,161 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:50:37,162 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:50:37,162 | ^~~~~~~ 2023-08-29T02:51:27,177 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:51:27,407 building 'MDAnalysis.lib.c_distances_openmp' extension 2023-08-29T02:51:27,408 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPARALLEL -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:51:27,730 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:51:27,731 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:51:27,731 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:51:27,731 from MDAnalysis/lib/c_distances_openmp.c:1199: 2023-08-29T02:51:27,731 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:51:27,731 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:51:27,731 | ^~~~~~~ 2023-08-29T02:51:41,023 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib -lm -lgomp -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -fopenmp 2023-08-29T02:51:41,188 building 'MDAnalysis.lib.qcprot' extension 2023-08-29T02:51:41,188 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.o -std=c99 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:51:41,521 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:51:41,521 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:51:41,522 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:51:41,522 from MDAnalysis/lib/qcprot.c:1182: 2023-08-29T02:51:41,522 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:51:41,522 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:51:41,523 | ^~~~~~~ 2023-08-29T02:51:41,609 MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’: 2023-08-29T02:51:41,612 MDAnalysis/lib/qcprot.c:5100:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:51:41,612 5100 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2023-08-29T02:51:41,612 | ^ 2023-08-29T02:51:41,616 MDAnalysis/lib/qcprot.c:5308:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:51:41,616 5308 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2023-08-29T02:51:41,617 | ^ 2023-08-29T02:51:56,152 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:51:56,285 building 'MDAnalysis.lib._transformations' extension 2023-08-29T02:51:56,286 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src 2023-08-29T02:51:56,286 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-08-29T02:51:56,287 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:51:56,602 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:51:56,602 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:51:56,602 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:51:56,603 from MDAnalysis/lib/src/transformations/transformations.c:73: 2023-08-29T02:51:56,603 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:51:56,603 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:51:56,603 | ^~~~~~~ 2023-08-29T02:51:56,664 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: 2023-08-29T02:51:56,664 MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,664 1845 | #pragma vector always 2023-08-29T02:51:56,664 | 2023-08-29T02:51:56,666 MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,667 1962 | #pragma vector always 2023-08-29T02:51:56,667 | 2023-08-29T02:51:56,667 MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,667 1986 | #pragma vector always 2023-08-29T02:51:56,667 | 2023-08-29T02:51:56,670 MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: 2023-08-29T02:51:56,671 MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] 2023-08-29T02:51:56,672 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { 2023-08-29T02:51:56,672 | ^~ 2023-08-29T02:51:56,672 In file included from /usr/include/python3.9/Python.h:97, 2023-08-29T02:51:56,672 from MDAnalysis/lib/src/transformations/transformations.c:68: 2023-08-29T02:51:56,672 /usr/include/python3.9/unicodeobject.h:177:43: note: declared here 2023-08-29T02:51:56,672 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( 2023-08-29T02:51:56,673 | ^~~~~~~~~~~~~~~~~ 2023-08-29T02:51:56,708 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: 2023-08-29T02:51:56,708 MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,708 3427 | #pragma vector always 2023-08-29T02:51:56,708 | 2023-08-29T02:51:56,711 MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,711 3508 | #pragma vector always 2023-08-29T02:51:56,711 | 2023-08-29T02:51:56,716 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: 2023-08-29T02:51:56,716 MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,716 3610 | #pragma vector always 2023-08-29T02:51:56,716 | 2023-08-29T02:51:56,717 MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,717 3615 | #pragma vector always 2023-08-29T02:51:56,717 | 2023-08-29T02:51:56,720 MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,721 3679 | #pragma vector always 2023-08-29T02:51:56,721 | 2023-08-29T02:51:56,721 MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-08-29T02:51:56,721 3684 | #pragma vector always 2023-08-29T02:51:56,721 | 2023-08-29T02:51:56,789 At top level: 2023-08-29T02:51:56,790 MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] 2023-08-29T02:51:56,790 910 | PyConverter_DoubleVector4Copy( 2023-08-29T02:51:56,790 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:51:56,790 MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] 2023-08-29T02:51:56,790 804 | PyConverter_DoubleArrayOrNone( 2023-08-29T02:51:56,790 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:51:56,790 MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] 2023-08-29T02:51:56,791 774 | PyConverter_DoubleArray( 2023-08-29T02:51:56,791 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:52:02,557 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:52:02,682 building 'MDAnalysis.lib.formats.libmdaxdr' extension 2023-08-29T02:52:02,683 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-08-29T02:52:02,685 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-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:52:03,011 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:52:03,011 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:52:03,011 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:52:03,012 from MDAnalysis/lib/formats/libmdaxdr.c:1209: 2023-08-29T02:52:03,012 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:52:03,012 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:52:03,012 | ^~~~~~~ 2023-08-29T02:52:03,045 In file included from MDAnalysis/lib/formats/libmdaxdr.c:1215: 2023-08-29T02:52:03,045 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:52:03,046 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:52:03,046 | 2023-08-29T02:52:03,047 In file included from MDAnalysis/lib/formats/libmdaxdr.c:1216: 2023-08-29T02:52:03,047 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:52:03,047 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:52:03,047 | 2023-08-29T02:52:03,047 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-08-29T02:52:03,048 from MDAnalysis/lib/formats/libmdaxdr.c:1216: 2023-08-29T02:52:03,048 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:52:03,048 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:52:03,048 | 2023-08-29T02:52:03,048 In file included from MDAnalysis/lib/formats/libmdaxdr.c:1217: 2023-08-29T02:52:03,048 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:52:03,048 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:52:03,049 | 2023-08-29T02:52:58,039 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-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:52:58,118 In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: 2023-08-29T02:52:58,118 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:52:58,118 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:52:58,118 | 2023-08-29T02:52:58,122 In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: 2023-08-29T02:52:58,122 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:52:58,123 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:52:58,123 | 2023-08-29T02:52:58,123 In file included from /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2023-08-29T02:52:58,123 from MDAnalysis/lib/formats/src/trr_seek.c:31: 2023-08-29T02:52:58,123 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:52:58,123 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:52:58,124 | 2023-08-29T02:52:58,125 MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’: 2023-08-29T02:52:58,126 MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable] 2023-08-29T02:52:58,126 39 | int result, framebytes, totalframebytes; 2023-08-29T02:52:58,127 | ^~~~~~~~~~~~~~~ 2023-08-29T02:52:58,127 MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable] 2023-08-29T02:52:58,127 38 | float time, lambda; 2023-08-29T02:52:58,127 | ^~~~~~ 2023-08-29T02:52:58,127 MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable] 2023-08-29T02:52:58,127 38 | float time, lambda; 2023-08-29T02:52:58,127 | ^~~~ 2023-08-29T02:52:58,229 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-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:52:58,345 In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: 2023-08-29T02:52:58,345 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:52:58,345 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:52:58,346 | 2023-08-29T02:52:58,354 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’: 2023-08-29T02:52:58,355 MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-08-29T02:52:58,355 501 | while (size >= num && num_of_bits < 32) 2023-08-29T02:52:58,355 | ^~ 2023-08-29T02:52:58,356 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’: 2023-08-29T02:52:58,356 MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:52:58,356 547 | while (bytes[num_of_bytes] >= num) 2023-08-29T02:52:58,357 | ^~ 2023-08-29T02:52:58,358 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’: 2023-08-29T02:52:58,358 MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-08-29T02:52:58,358 656 | if (num_of_bits >= num_of_bytes * 8) 2023-08-29T02:52:58,359 | ^~ 2023-08-29T02:52:58,359 MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-08-29T02:52:58,359 658 | for (i = 0; i < num_of_bytes; i++) 2023-08-29T02:52:58,359 | ^ 2023-08-29T02:52:58,360 MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-08-29T02:52:58,360 666 | for (i = 0; i < num_of_bytes-1; i++) 2023-08-29T02:52:58,360 | ^ 2023-08-29T02:52:58,361 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’: 2023-08-29T02:52:58,361 MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:52:58,361 706 | if (lastbits < num_of_bits) 2023-08-29T02:52:58,362 | ^ 2023-08-29T02:52:58,363 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-08-29T02:52:58,364 MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:52:58,364 816 | if(size3>xfp->buf1size) 2023-08-29T02:52:58,364 | ^ 2023-08-29T02:52:58,366 MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:52:58,366 868 | maxidx = (LASTIDXxfp->buf1size) 2023-08-29T02:52:58,373 | ^ 2023-08-29T02:52:58,377 MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-08-29T02:52:58,377 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2023-08-29T02:52:58,378 | ^ 2023-08-29T02:52:58,378 MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:52:58,379 1141 | maxidx = (LASTIDXxfp->buf1size) 2023-08-29T02:52:58,386 | ^ 2023-08-29T02:52:58,388 MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:52:58,389 1368 | maxidx = (LASTIDXxfp->buf1size) { 2023-08-29T02:52:58,396 | ^ 2023-08-29T02:52:58,403 MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-08-29T02:52:58,403 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2023-08-29T02:52:58,403 | ^ 2023-08-29T02:52:58,404 MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-08-29T02:52:58,404 1624 | maxidx = (LASTIDX maxsize) 2023-08-29T02:53:00,074 | ^ 2023-08-29T02:53:00,075 MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here 2023-08-29T02:53:00,076 2335 | unsigned int size; 2023-08-29T02:53:00,076 | ^~~~ 2023-08-29T02:53:00,507 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-08-29T02:53:00,508 MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-08-29T02:53:00,508 1157 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2023-08-29T02:53:00,509 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-08-29T02:53:00,509 MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-08-29T02:53:00,510 1156 | abs(thiscoord[1] - prevcoord[1]) < larger && 2023-08-29T02:53:00,510 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-08-29T02:53:00,510 MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-08-29T02:53:00,511 1155 | abs(thiscoord[0] - prevcoord[0]) < larger && 2023-08-29T02:53:00,511 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-08-29T02:53:01,269 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-08-29T02:53:01,270 MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-08-29T02:53:01,271 1639 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2023-08-29T02:53:01,271 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-08-29T02:53:01,272 MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-08-29T02:53:01,272 1638 | abs(thiscoord[1] - prevcoord[1]) < larger && 2023-08-29T02:53:01,272 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-08-29T02:53:01,273 MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-08-29T02:53:01,273 1637 | abs(thiscoord[0] - prevcoord[0]) < larger && 2023-08-29T02:53:01,273 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-08-29T02:53:02,318 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-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:53:02,388 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: 2023-08-29T02:53:02,388 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:02,388 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:02,389 | 2023-08-29T02:53:02,392 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2023-08-29T02:53:02,392 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:02,392 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:02,393 | 2023-08-29T02:53:02,393 In file included from /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2023-08-29T02:53:02,393 from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2023-08-29T02:53:02,393 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:02,393 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:02,393 | 2023-08-29T02:53:02,394 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’: 2023-08-29T02:53:02,394 MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-08-29T02:53:02,395 78 | if (slen != strlen(version) + 1) 2023-08-29T02:53:02,395 | ^~ 2023-08-29T02:53:02,395 MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-08-29T02:53:02,395 86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) 2023-08-29T02:53:02,395 | ^~ 2023-08-29T02:53:02,410 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’: 2023-08-29T02:53:02,411 MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized] 2023-08-29T02:53:02,411 408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); 2023-08-29T02:53:02,411 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:53:03,521 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-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:53:03,568 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: 2023-08-29T02:53:03,568 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:03,568 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:03,568 | 2023-08-29T02:53:03,579 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2023-08-29T02:53:03,580 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:03,580 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:03,580 | 2023-08-29T02:53:03,580 In file included from /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-08-29T02:53:03,581 from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2023-08-29T02:53:03,581 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:03,581 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:03,581 | 2023-08-29T02:53:03,699 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-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:53:03,746 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: 2023-08-29T02:53:03,747 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:03,747 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:03,747 | 2023-08-29T02:53:03,757 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2023-08-29T02:53:03,757 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:03,757 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:03,757 | 2023-08-29T02:53:03,757 In file included from /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-08-29T02:53:03,758 from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2023-08-29T02:53:03,758 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-08-29T02:53:03,758 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-08-29T02:53:03,758 | 2023-08-29T02:53:03,911 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:53:04,168 building 'MDAnalysis.lib.formats.cython_util' extension 2023-08-29T02:53:04,168 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.o -std=c99 -O3 -funroll-loops -fsigned-zeros 2023-08-29T02:53:04,489 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:53:04,490 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:53:04,490 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:53:04,490 from MDAnalysis/lib/formats/cython_util.c:1199: 2023-08-29T02:53:04,490 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:53:04,490 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:53:04,490 | ^~~~~~~ 2023-08-29T02:53:29,038 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:53:29,197 building 'MDAnalysis.analysis.encore.cutils' extension 2023-08-29T02:53:29,198 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-08-29T02:53:29,198 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-08-29T02:53:29,199 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.o -std=c99 -funroll-loops -fsigned-zeros -O3 2023-08-29T02:53:29,510 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:53:29,510 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:53:29,510 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:53:29,511 from MDAnalysis/analysis/encore/cutils.c:1182: 2023-08-29T02:53:29,511 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:53:29,511 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:53:29,511 | ^~~~~~~ 2023-08-29T02:53:34,759 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:53:34,881 building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension 2023-08-29T02:53:34,882 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-08-29T02:53:34,883 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-08-29T02:53:34,884 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -funroll-loops -fsigned-zeros -O3 2023-08-29T02:53:35,209 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:53:35,209 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:53:35,209 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:53:35,209 from MDAnalysis/analysis/encore/clustering/affinityprop.c:1188: 2023-08-29T02:53:35,210 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:53:35,210 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:53:35,210 | ^~~~~~~ 2023-08-29T02:53:51,089 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -funroll-loops -fsigned-zeros -O3 2023-08-29T02:53:52,119 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:53:52,256 building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension 2023-08-29T02:53:52,257 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:53:52,258 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-08-29T02:53:52,259 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -funroll-loops -fsigned-zeros -O3 2023-08-29T02:53:52,974 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/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 -funroll-loops -fsigned-zeros -O3 2023-08-29T02:53:53,288 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:53:53,289 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:53:53,289 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:53:53,289 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:1188: 2023-08-29T02:53:53,289 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:53:53,289 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:53:53,289 | ^~~~~~~ 2023-08-29T02:54:01,128 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:54:01,269 building 'MDAnalysis.lib._cutil' extension 2023-08-29T02:54:01,269 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.o -O3 -funroll-loops -fsigned-zeros -std=c++11 2023-08-29T02:54:01,520 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:54:01,521 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:54:01,521 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:54:01,521 from MDAnalysis/lib/_cutil.cpp:1200: 2023-08-29T02:54:01,521 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:54:01,521 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:54:01,521 | ^~~~~~~ 2023-08-29T02:54:04,611 In file included from MDAnalysis/lib/_cutil.cpp:1226: 2023-08-29T02:54:04,611 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:827:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,611 827 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,611 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,612 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:791:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,612 791 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,612 | ^~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,612 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:764:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,612 764 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,613 | ^~~~~~~~~~~~~~ 2023-08-29T02:54:04,613 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:689:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,613 689 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,613 | ^~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,613 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:647:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,613 647 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,614 | ^~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,614 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:618:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,614 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,614 | ^~~~~~~~~~~ 2023-08-29T02:54:04,615 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:596:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,615 596 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,615 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,615 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:573:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,615 573 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,615 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,615 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:557:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,616 557 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2023-08-29T02:54:04,616 | ^~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,616 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:505:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,616 505 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-08-29T02:54:04,616 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,617 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:472:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,617 472 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2023-08-29T02:54:04,617 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,617 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:448:13: warning: ‘void _calc_self_distance_array(float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,617 448 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2023-08-29T02:54:04,617 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,617 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:424:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,618 424 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-08-29T02:54:04,618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,618 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:399:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,618 399 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2023-08-29T02:54:04,618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,618 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:381:13: warning: ‘void _calc_distance_array(float (*)[3], uint64_t, float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,618 381 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2023-08-29T02:54:04,619 | ^~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:54:04,619 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:116:13: warning: ‘void _ortho_pbc(float (*)[3], uint64_t, float*)’ defined but not used [-Wunused-function] 2023-08-29T02:54:04,619 116 | static void _ortho_pbc(coordinate* coords, uint64_t numcoords, float* box) 2023-08-29T02:54:04,619 | ^~~~~~~~~~ 2023-08-29T02:54:41,127 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:54:41,481 building 'MDAnalysis.lib._augment' extension 2023-08-29T02:54:41,482 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.o -O3 -funroll-loops -fsigned-zeros -std=c++11 2023-08-29T02:54:41,751 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:54:41,752 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:54:41,752 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:54:41,752 from MDAnalysis/lib/_augment.cpp:1195: 2023-08-29T02:54:41,752 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:54:41,752 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:54:41,752 | ^~~~~~~ 2023-08-29T02:55:12,684 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:55:13,003 building 'MDAnalysis.lib.nsgrid' extension 2023-08-29T02:55:13,004 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.o -O3 -funroll-loops -fsigned-zeros -std=c++11 2023-08-29T02:55:15,747 In file included from MDAnalysis/lib/nsgrid.cpp:1193: 2023-08-29T02:55:15,747 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:827:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,747 827 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,747 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,748 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:791:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,748 791 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,748 | ^~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,748 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:764:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,748 764 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,749 | ^~~~~~~~~~~~~~ 2023-08-29T02:55:15,749 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:689:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,749 689 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,749 | ^~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,749 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:647:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,749 647 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,750 | ^~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,750 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:618:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,750 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,750 | ^~~~~~~~~~~ 2023-08-29T02:55:15,750 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:596:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,751 596 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,751 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,751 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:573:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,751 573 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,751 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,751 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:557:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,751 557 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2023-08-29T02:55:15,751 | ^~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,752 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:505:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,752 505 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-08-29T02:55:15,752 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,752 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:472:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,752 472 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2023-08-29T02:55:15,752 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,752 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:448:13: warning: ‘void _calc_self_distance_array(float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,753 448 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2023-08-29T02:55:15,753 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,753 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:424:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,753 424 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-08-29T02:55:15,753 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,753 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:399:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,753 399 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2023-08-29T02:55:15,754 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:15,754 /tmp/pip-wheel-od_u39vf/mdanalysis_b168a8018b10456492988bc6604b17f5/MDAnalysis/lib/include/calc_distances.h:381:13: warning: ‘void _calc_distance_array(float (*)[3], uint64_t, float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-08-29T02:55:15,754 381 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2023-08-29T02:55:15,754 | ^~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:47,439 In file included from /usr/include/c++/10/vector:72, 2023-08-29T02:55:47,439 from MDAnalysis/lib/nsgrid.cpp:1191: 2023-08-29T02:55:47,440 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-08-29T02:55:47,440 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-08-29T02:55:47,440 426 | vector<_Tp, _Alloc>:: 2023-08-29T02:55:47,440 | ^~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:47,476 In file included from /usr/include/c++/10/vector:67, 2023-08-29T02:55:47,476 from MDAnalysis/lib/nsgrid.cpp:1191: 2023-08-29T02:55:47,476 /usr/include/c++/10/bits/stl_vector.h: In function ‘void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_add_neighbors(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, int, int, double)’: 2023-08-29T02:55:47,476 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-08-29T02:55:47,476 1198 | _M_realloc_insert(end(), __x); 2023-08-29T02:55:47,476 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-08-29T02:55:47,516 In file included from /usr/include/c++/10/vector:72, 2023-08-29T02:55:47,517 from MDAnalysis/lib/nsgrid.cpp:1191: 2023-08-29T02:55:47,517 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-08-29T02:55:47,517 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-08-29T02:55:47,517 426 | vector<_Tp, _Alloc>:: 2023-08-29T02:55:47,517 | ^~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:47,765 /usr/include/c++/10/bits/vector.tcc: In function ‘PyObject* __pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults__set_state(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, PyObject*)’: 2023-08-29T02:55:47,766 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-08-29T02:55:47,766 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-08-29T02:55:47,766 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-08-29T02:55:51,593 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:55:51,945 building 'MDAnalysis.coordinates.timestep' extension 2023-08-29T02:55:51,946 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-08-29T02:55:51,947 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.o -O3 -funroll-loops -fsigned-zeros -std=c++11 2023-08-29T02:55:52,189 In file included from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960, 2023-08-29T02:55:52,190 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-08-29T02:55:52,190 from /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, 2023-08-29T02:55:52,190 from MDAnalysis/coordinates/timestep.cpp:1196: 2023-08-29T02:55:52,190 /tmp/pip-build-env-5tvu3e23/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-08-29T02:55:52,190 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-08-29T02:55:52,190 | ^~~~~~~ 2023-08-29T02:56:16,791 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so 2023-08-29T02:56:17,009 installing to build/bdist.linux-armv7l/wheel 2023-08-29T02:56:17,010 running install 2023-08-29T02:56:17,036 running install_lib 2023-08-29T02:56:17,042 creating build/bdist.linux-armv7l 2023-08-29T02:56:17,043 creating build/bdist.linux-armv7l/wheel 2023-08-29T02:56:17,044 creating build/bdist.linux-armv7l/wheel/MDAnalysis 2023-08-29T02:56:17,046 creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-08-29T02:56:17,047 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-08-29T02:56:17,050 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-08-29T02:56:17,052 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-08-29T02:56:17,054 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-08-29T02:56:17,056 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-08-29T02:56:17,058 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-08-29T02:56:17,060 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-08-29T02:56:17,062 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-08-29T02:56:17,064 creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-08-29T02:56:17,065 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-08-29T02:56:17,069 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-08-29T02:56:17,070 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-08-29T02:56:17,074 creating build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-08-29T02:56:17,075 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-08-29T02:56:17,077 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-08-29T02:56:17,080 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-08-29T02:56:17,084 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-08-29T02:56:17,086 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-08-29T02:56:17,088 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-08-29T02:56:17,091 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-08-29T02:56:17,093 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-08-29T02:56:17,096 creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-08-29T02:56:17,097 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-08-29T02:56:17,099 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-08-29T02:56:17,101 creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-08-29T02:56:17,102 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-08-29T02:56:17,105 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-08-29T02:56:17,107 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-08-29T02:56:17,111 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-08-29T02:56:17,114 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-08-29T02:56:17,117 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,118 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,121 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,123 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,125 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,128 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,130 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,132 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,134 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,136 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,138 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,140 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,144 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,147 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,150 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,153 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,157 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,159 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,162 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,164 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,167 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,199 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,219 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,222 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,224 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,227 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,230 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,233 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,236 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,239 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,242 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,244 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,247 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,250 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,253 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,256 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,260 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,263 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-08-29T02:56:17,266 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,267 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,270 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,274 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,276 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,283 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,292 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:56:17,292 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:56:17,295 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-08-29T02:56:17,296 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-08-29T02:56:17,298 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:56:17,301 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:56:17,302 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:56:17,305 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:56:17,314 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-08-29T02:56:17,315 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-08-29T02:56:17,316 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-08-29T02:56:17,328 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,330 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,332 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,336 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,338 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-08-29T02:56:17,340 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src 2023-08-29T02:56:17,341 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src 2023-08-29T02:56:17,343 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-08-29T02:56:17,353 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-08-29T02:56:17,356 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-08-29T02:56:17,358 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-08-29T02:56:17,369 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-08-29T02:56:17,372 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-08-29T02:56:17,374 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-08-29T02:56:17,376 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include 2023-08-29T02:56:17,377 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include 2023-08-29T02:56:17,379 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,381 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,384 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-08-29T02:56:17,387 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-08-29T02:56:17,388 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-08-29T02:56:17,390 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-08-29T02:56:17,393 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-08-29T02:56:17,396 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-08-29T02:56:17,399 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-08-29T02:56:17,400 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-08-29T02:56:17,403 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-08-29T02:56:17,405 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,409 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,412 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,415 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,418 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,421 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:56:17,422 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:56:17,429 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:56:17,432 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:56:17,435 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-08-29T02:56:17,437 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,440 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/msd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,443 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,446 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,449 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-08-29T02:56:17,450 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-08-29T02:56:17,454 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-08-29T02:56:17,456 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-08-29T02:56:17,459 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-08-29T02:56:17,461 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,465 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,467 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,470 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,472 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/atomicdistances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,475 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,477 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,480 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,482 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,487 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,489 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/bat.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,492 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,496 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-08-29T02:56:17,497 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-08-29T02:56:17,499 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-08-29T02:56:17,501 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-08-29T02:56:17,504 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,505 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,508 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,510 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,514 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-08-29T02:56:17,515 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-08-29T02:56:17,517 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-08-29T02:56:17,519 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-08-29T02:56:17,522 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-08-29T02:56:17,525 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,528 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,530 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,532 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,535 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,537 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,540 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,542 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,544 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,547 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,550 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,552 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,555 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,558 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,560 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,564 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,566 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,568 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,571 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,573 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,575 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,578 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,580 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,582 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,585 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-08-29T02:56:17,588 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,589 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,593 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis 2023-08-29T02:56:17,593 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis 2023-08-29T02:56:17,596 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,616 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,642 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src 2023-08-29T02:56:17,644 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-08-29T02:56:17,645 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-08-29T02:56:17,649 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-08-29T02:56:17,651 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-08-29T02:56:17,653 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,656 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,659 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,682 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,721 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,750 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,752 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,754 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,775 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,786 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_distopia.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,788 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,791 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,828 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,830 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,837 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,840 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:17,844 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,845 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,847 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,881 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,884 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,913 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-08-29T02:56:17,914 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-08-29T02:56:17,918 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-08-29T02:56:17,920 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-08-29T02:56:17,923 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-08-29T02:56:17,925 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-08-29T02:56:17,927 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,947 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,949 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,952 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,954 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,955 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,957 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:17,993 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:18,014 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-08-29T02:56:18,041 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,042 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,044 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,047 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,049 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,051 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,053 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,056 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,057 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-08-29T02:56:18,060 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,062 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,064 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,075 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,078 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,082 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/correlations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,084 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,087 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,090 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,129 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,153 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include 2023-08-29T02:56:18,154 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include 2023-08-29T02:56:18,157 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,159 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-08-29T02:56:18,170 creating build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,171 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,175 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,179 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,182 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,186 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,190 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,192 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/accessors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,194 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,197 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-08-29T02:56:18,200 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-08-29T02:56:18,202 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-08-29T02:56:18,205 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-08-29T02:56:18,207 creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,208 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,211 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,213 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,215 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/nojump.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,218 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,220 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,222 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,225 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/wrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,227 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-08-29T02:56:18,229 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-08-29T02:56:18,231 running install_egg_info 2023-08-29T02:56:18,237 Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-2.6.1-py3.9.egg-info 2023-08-29T02:56:18,251 running install_scripts 2023-08-29T02:56:18,318 creating build/bdist.linux-armv7l/wheel/MDAnalysis-2.6.1.dist-info/WHEEL 2023-08-29T02:56:18,320 creating '/tmp/pip-wheel-15n27tuo/.tmp-vi9bed5t/MDAnalysis-2.6.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-08-29T02:56:18,323 adding 'MDAnalysis/__init__.py' 2023-08-29T02:56:18,325 adding 'MDAnalysis/authors.py' 2023-08-29T02:56:18,326 adding 'MDAnalysis/due.py' 2023-08-29T02:56:18,328 adding 'MDAnalysis/exceptions.py' 2023-08-29T02:56:18,330 adding 'MDAnalysis/units.py' 2023-08-29T02:56:18,332 adding 'MDAnalysis/version.py' 2023-08-29T02:56:18,334 adding 'MDAnalysis/analysis/__init__.py' 2023-08-29T02:56:18,342 adding 'MDAnalysis/analysis/align.py' 2023-08-29T02:56:18,344 adding 'MDAnalysis/analysis/atomicdistances.py' 2023-08-29T02:56:18,347 adding 'MDAnalysis/analysis/base.py' 2023-08-29T02:56:18,350 adding 'MDAnalysis/analysis/bat.py' 2023-08-29T02:56:18,353 adding 'MDAnalysis/analysis/contacts.py' 2023-08-29T02:56:18,359 adding 'MDAnalysis/analysis/density.py' 2023-08-29T02:56:18,361 adding 'MDAnalysis/analysis/dielectric.py' 2023-08-29T02:56:18,363 adding 'MDAnalysis/analysis/diffusionmap.py' 2023-08-29T02:56:18,366 adding 'MDAnalysis/analysis/dihedrals.py' 2023-08-29T02:56:18,368 adding 'MDAnalysis/analysis/distances.py' 2023-08-29T02:56:18,371 adding 'MDAnalysis/analysis/gnm.py' 2023-08-29T02:56:18,374 adding 'MDAnalysis/analysis/helix_analysis.py' 2023-08-29T02:56:18,376 adding 'MDAnalysis/analysis/leaflet.py' 2023-08-29T02:56:18,378 adding 'MDAnalysis/analysis/lineardensity.py' 2023-08-29T02:56:18,381 adding 'MDAnalysis/analysis/msd.py' 2023-08-29T02:56:18,383 adding 'MDAnalysis/analysis/nucleicacids.py' 2023-08-29T02:56:18,385 adding 'MDAnalysis/analysis/nuclinfo.py' 2023-08-29T02:56:18,390 adding 'MDAnalysis/analysis/pca.py' 2023-08-29T02:56:18,392 adding 'MDAnalysis/analysis/polymer.py' 2023-08-29T02:56:18,402 adding 'MDAnalysis/analysis/psa.py' 2023-08-29T02:56:18,405 adding 'MDAnalysis/analysis/rdf.py' 2023-08-29T02:56:18,410 adding 'MDAnalysis/analysis/rms.py' 2023-08-29T02:56:18,415 adding 'MDAnalysis/analysis/waterdynamics.py' 2023-08-29T02:56:18,417 adding 'MDAnalysis/analysis/data/__init__.py' 2023-08-29T02:56:18,419 adding 'MDAnalysis/analysis/data/filenames.py' 2023-08-29T02:56:18,422 adding 'MDAnalysis/analysis/data/janin_ref_data.npy' 2023-08-29T02:56:18,428 adding 'MDAnalysis/analysis/data/rama_ref_data.npy' 2023-08-29T02:56:18,430 adding 'MDAnalysis/analysis/encore/__init__.py' 2023-08-29T02:56:18,432 adding 'MDAnalysis/analysis/encore/bootstrap.py' 2023-08-29T02:56:18,434 adding 'MDAnalysis/analysis/encore/confdistmatrix.py' 2023-08-29T02:56:18,436 adding 'MDAnalysis/analysis/encore/covariance.py' 2023-08-29T02:56:18,470 adding 'MDAnalysis/analysis/encore/cutils.c' 2023-08-29T02:56:18,537 adding 'MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:18,540 adding 'MDAnalysis/analysis/encore/cutils.pyx' 2023-08-29T02:56:18,547 adding 'MDAnalysis/analysis/encore/similarity.py' 2023-08-29T02:56:18,549 adding 'MDAnalysis/analysis/encore/utils.py' 2023-08-29T02:56:18,552 adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' 2023-08-29T02:56:18,554 adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' 2023-08-29T02:56:18,556 adding 'MDAnalysis/analysis/encore/clustering/__init__.py' 2023-08-29T02:56:18,600 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' 2023-08-29T02:56:18,738 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:18,744 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' 2023-08-29T02:56:18,746 adding 'MDAnalysis/analysis/encore/clustering/cluster.py' 2023-08-29T02:56:18,747 adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' 2023-08-29T02:56:18,750 adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' 2023-08-29T02:56:18,752 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' 2023-08-29T02:56:18,753 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' 2023-08-29T02:56:18,755 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' 2023-08-29T02:56:18,791 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' 2023-08-29T02:56:18,886 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:18,890 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' 2023-08-29T02:56:18,892 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' 2023-08-29T02:56:18,894 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' 2023-08-29T02:56:18,896 adding 'MDAnalysis/analysis/hbonds/__init__.py' 2023-08-29T02:56:18,897 adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' 2023-08-29T02:56:18,900 adding 'MDAnalysis/analysis/hole2/__init__.py' 2023-08-29T02:56:18,906 adding 'MDAnalysis/analysis/hole2/hole.py' 2023-08-29T02:56:18,907 adding 'MDAnalysis/analysis/hole2/templates.py' 2023-08-29T02:56:18,910 adding 'MDAnalysis/analysis/hole2/utils.py' 2023-08-29T02:56:18,912 adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' 2023-08-29T02:56:18,917 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' 2023-08-29T02:56:18,920 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' 2023-08-29T02:56:18,930 adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' 2023-08-29T02:56:18,932 adding 'MDAnalysis/analysis/legacy/__init__.py' 2023-08-29T02:56:18,936 adding 'MDAnalysis/analysis/legacy/x3dna.py' 2023-08-29T02:56:18,939 adding 'MDAnalysis/auxiliary/EDR.py' 2023-08-29T02:56:18,942 adding 'MDAnalysis/auxiliary/XVG.py' 2023-08-29T02:56:18,945 adding 'MDAnalysis/auxiliary/__init__.py' 2023-08-29T02:56:18,950 adding 'MDAnalysis/auxiliary/base.py' 2023-08-29T02:56:18,952 adding 'MDAnalysis/auxiliary/core.py' 2023-08-29T02:56:18,954 adding 'MDAnalysis/converters/OpenMM.py' 2023-08-29T02:56:18,956 adding 'MDAnalysis/converters/OpenMMParser.py' 2023-08-29T02:56:18,958 adding 'MDAnalysis/converters/ParmEd.py' 2023-08-29T02:56:18,960 adding 'MDAnalysis/converters/ParmEdParser.py' 2023-08-29T02:56:18,965 adding 'MDAnalysis/converters/RDKit.py' 2023-08-29T02:56:18,967 adding 'MDAnalysis/converters/RDKitParser.py' 2023-08-29T02:56:18,969 adding 'MDAnalysis/converters/__init__.py' 2023-08-29T02:56:18,972 adding 'MDAnalysis/coordinates/CRD.py' 2023-08-29T02:56:18,974 adding 'MDAnalysis/coordinates/DCD.py' 2023-08-29T02:56:18,976 adding 'MDAnalysis/coordinates/DLPoly.py' 2023-08-29T02:56:18,978 adding 'MDAnalysis/coordinates/DMS.py' 2023-08-29T02:56:18,980 adding 'MDAnalysis/coordinates/FHIAIMS.py' 2023-08-29T02:56:18,982 adding 'MDAnalysis/coordinates/GMS.py' 2023-08-29T02:56:18,984 adding 'MDAnalysis/coordinates/GRO.py' 2023-08-29T02:56:18,986 adding 'MDAnalysis/coordinates/GSD.py' 2023-08-29T02:56:18,994 adding 'MDAnalysis/coordinates/H5MD.py' 2023-08-29T02:56:18,996 adding 'MDAnalysis/coordinates/INPCRD.py' 2023-08-29T02:56:19,000 adding 'MDAnalysis/coordinates/LAMMPS.py' 2023-08-29T02:56:19,001 adding 'MDAnalysis/coordinates/MMTF.py' 2023-08-29T02:56:19,003 adding 'MDAnalysis/coordinates/MOL2.py' 2023-08-29T02:56:19,005 adding 'MDAnalysis/coordinates/NAMDBIN.py' 2023-08-29T02:56:19,012 adding 'MDAnalysis/coordinates/PDB.py' 2023-08-29T02:56:19,015 adding 'MDAnalysis/coordinates/PDBQT.py' 2023-08-29T02:56:19,017 adding 'MDAnalysis/coordinates/PQR.py' 2023-08-29T02:56:19,018 adding 'MDAnalysis/coordinates/ParmEd.py' 2023-08-29T02:56:19,021 adding 'MDAnalysis/coordinates/TNG.py' 2023-08-29T02:56:19,027 adding 'MDAnalysis/coordinates/TRJ.py' 2023-08-29T02:56:19,029 adding 'MDAnalysis/coordinates/TRR.py' 2023-08-29T02:56:19,032 adding 'MDAnalysis/coordinates/TRZ.py' 2023-08-29T02:56:19,034 adding 'MDAnalysis/coordinates/TXYZ.py' 2023-08-29T02:56:19,036 adding 'MDAnalysis/coordinates/XDR.py' 2023-08-29T02:56:19,038 adding 'MDAnalysis/coordinates/XTC.py' 2023-08-29T02:56:19,040 adding 'MDAnalysis/coordinates/XYZ.py' 2023-08-29T02:56:19,045 adding 'MDAnalysis/coordinates/__init__.py' 2023-08-29T02:56:19,053 adding 'MDAnalysis/coordinates/base.py' 2023-08-29T02:56:19,056 adding 'MDAnalysis/coordinates/chain.py' 2023-08-29T02:56:19,059 adding 'MDAnalysis/coordinates/chemfiles.py' 2023-08-29T02:56:19,061 adding 'MDAnalysis/coordinates/core.py' 2023-08-29T02:56:19,064 adding 'MDAnalysis/coordinates/memory.py' 2023-08-29T02:56:19,066 adding 'MDAnalysis/coordinates/null.py' 2023-08-29T02:56:19,143 adding 'MDAnalysis/coordinates/timestep.cpp' 2023-08-29T02:56:19,400 adding 'MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:19,409 adding 'MDAnalysis/coordinates/timestep.pxd' 2023-08-29T02:56:19,413 adding 'MDAnalysis/coordinates/timestep.pyx' 2023-08-29T02:56:19,415 adding 'MDAnalysis/core/__init__.py' 2023-08-29T02:56:19,417 adding 'MDAnalysis/core/_get_readers.py' 2023-08-29T02:56:19,419 adding 'MDAnalysis/core/accessors.py' 2023-08-29T02:56:19,440 adding 'MDAnalysis/core/groups.py' 2023-08-29T02:56:19,448 adding 'MDAnalysis/core/selection.py' 2023-08-29T02:56:19,451 adding 'MDAnalysis/core/topology.py' 2023-08-29T02:56:19,462 adding 'MDAnalysis/core/topologyattrs.py' 2023-08-29T02:56:19,467 adding 'MDAnalysis/core/topologyobjects.py' 2023-08-29T02:56:19,475 adding 'MDAnalysis/core/universe.py' 2023-08-29T02:56:19,478 adding 'MDAnalysis/lib/NeighborSearch.py' 2023-08-29T02:56:19,479 adding 'MDAnalysis/lib/__init__.py' 2023-08-29T02:56:19,574 adding 'MDAnalysis/lib/_augment.cpp' 2023-08-29T02:56:19,873 adding 'MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:19,884 adding 'MDAnalysis/lib/_augment.pyx' 2023-08-29T02:56:19,987 adding 'MDAnalysis/lib/_cutil.cpp' 2023-08-29T02:56:20,375 adding 'MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:20,388 adding 'MDAnalysis/lib/_cutil.pxd' 2023-08-29T02:56:20,391 adding 'MDAnalysis/lib/_cutil.pyx' 2023-08-29T02:56:20,392 adding 'MDAnalysis/lib/_distopia.py' 2023-08-29T02:56:20,447 adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:20,566 adding 'MDAnalysis/lib/c_distances.c' 2023-08-29T02:56:20,967 adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:20,981 adding 'MDAnalysis/lib/c_distances.pyx' 2023-08-29T02:56:21,020 adding 'MDAnalysis/lib/c_distances_openmp.c' 2023-08-29T02:56:21,141 adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:21,146 adding 'MDAnalysis/lib/c_distances_openmp.pyx' 2023-08-29T02:56:21,148 adding 'MDAnalysis/lib/correlations.py' 2023-08-29T02:56:21,155 adding 'MDAnalysis/lib/distances.py' 2023-08-29T02:56:21,157 adding 'MDAnalysis/lib/log.py' 2023-08-29T02:56:21,160 adding 'MDAnalysis/lib/mdamath.py' 2023-08-29T02:56:21,269 adding 'MDAnalysis/lib/nsgrid.cpp' 2023-08-29T02:56:21,651 adding 'MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:21,666 adding 'MDAnalysis/lib/nsgrid.pyx' 2023-08-29T02:56:21,668 adding 'MDAnalysis/lib/picklable_file_io.py' 2023-08-29T02:56:21,670 adding 'MDAnalysis/lib/pkdtree.py' 2023-08-29T02:56:21,715 adding 'MDAnalysis/lib/qcprot.c' 2023-08-29T02:56:21,822 adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:21,828 adding 'MDAnalysis/lib/qcprot.pyx' 2023-08-29T02:56:21,835 adding 'MDAnalysis/lib/transformations.py' 2023-08-29T02:56:21,847 adding 'MDAnalysis/lib/util.py' 2023-08-29T02:56:21,849 adding 'MDAnalysis/lib/formats/__init__.py' 2023-08-29T02:56:21,938 adding 'MDAnalysis/lib/formats/cython_util.c' 2023-08-29T02:56:22,178 adding 'MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:22,187 adding 'MDAnalysis/lib/formats/cython_util.pxd' 2023-08-29T02:56:22,188 adding 'MDAnalysis/lib/formats/cython_util.pyx' 2023-08-29T02:56:22,313 adding 'MDAnalysis/lib/formats/libdcd.c' 2023-08-29T02:56:22,737 adding 'MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:22,752 adding 'MDAnalysis/lib/formats/libdcd.pxd' 2023-08-29T02:56:22,755 adding 'MDAnalysis/lib/formats/libdcd.pyx' 2023-08-29T02:56:22,880 adding 'MDAnalysis/lib/formats/libmdaxdr.c' 2023-08-29T02:56:23,344 adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so' 2023-08-29T02:56:23,359 adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' 2023-08-29T02:56:23,363 adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' 2023-08-29T02:56:23,365 adding 'MDAnalysis/lib/formats/include/endianswap.h' 2023-08-29T02:56:23,367 adding 'MDAnalysis/lib/formats/include/fastio.h' 2023-08-29T02:56:23,371 adding 'MDAnalysis/lib/formats/include/readdcd.h' 2023-08-29T02:56:23,372 adding 'MDAnalysis/lib/formats/include/trr_seek.h' 2023-08-29T02:56:23,375 adding 'MDAnalysis/lib/formats/include/xdrfile.h' 2023-08-29T02:56:23,376 adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' 2023-08-29T02:56:23,378 adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' 2023-08-29T02:56:23,379 adding 'MDAnalysis/lib/formats/include/xtc_seek.h' 2023-08-29T02:56:23,381 adding 'MDAnalysis/lib/formats/src/trr_seek.c' 2023-08-29T02:56:23,388 adding 'MDAnalysis/lib/formats/src/xdrfile.c' 2023-08-29T02:56:23,390 adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' 2023-08-29T02:56:23,392 adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' 2023-08-29T02:56:23,393 adding 'MDAnalysis/lib/formats/src/xtc_seek.c' 2023-08-29T02:56:23,397 adding 'MDAnalysis/lib/include/calc_distances.h' 2023-08-29T02:56:23,399 adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' 2023-08-29T02:56:23,401 adding 'MDAnalysis/lib/src/transformations/AUTHOR' 2023-08-29T02:56:23,402 adding 'MDAnalysis/lib/src/transformations/LICENCE' 2023-08-29T02:56:23,412 adding 'MDAnalysis/lib/src/transformations/transformations.c' 2023-08-29T02:56:23,415 adding 'MDAnalysis/selections/__init__.py' 2023-08-29T02:56:23,417 adding 'MDAnalysis/selections/base.py' 2023-08-29T02:56:23,419 adding 'MDAnalysis/selections/charmm.py' 2023-08-29T02:56:23,420 adding 'MDAnalysis/selections/gromacs.py' 2023-08-29T02:56:23,421 adding 'MDAnalysis/selections/jmol.py' 2023-08-29T02:56:23,423 adding 'MDAnalysis/selections/pymol.py' 2023-08-29T02:56:23,424 adding 'MDAnalysis/selections/vmd.py' 2023-08-29T02:56:23,426 adding 'MDAnalysis/tests/__init__.py' 2023-08-29T02:56:23,428 adding 'MDAnalysis/tests/datafiles.py' 2023-08-29T02:56:23,430 adding 'MDAnalysis/topology/CRDParser.py' 2023-08-29T02:56:23,432 adding 'MDAnalysis/topology/DLPolyParser.py' 2023-08-29T02:56:23,433 adding 'MDAnalysis/topology/DMSParser.py' 2023-08-29T02:56:23,435 adding 'MDAnalysis/topology/ExtendedPDBParser.py' 2023-08-29T02:56:23,436 adding 'MDAnalysis/topology/FHIAIMSParser.py' 2023-08-29T02:56:23,438 adding 'MDAnalysis/topology/GMSParser.py' 2023-08-29T02:56:23,440 adding 'MDAnalysis/topology/GROParser.py' 2023-08-29T02:56:23,441 adding 'MDAnalysis/topology/GSDParser.py' 2023-08-29T02:56:23,443 adding 'MDAnalysis/topology/HoomdXMLParser.py' 2023-08-29T02:56:23,446 adding 'MDAnalysis/topology/ITPParser.py' 2023-08-29T02:56:23,449 adding 'MDAnalysis/topology/LAMMPSParser.py' 2023-08-29T02:56:23,451 adding 'MDAnalysis/topology/MMTFParser.py' 2023-08-29T02:56:23,453 adding 'MDAnalysis/topology/MOL2Parser.py' 2023-08-29T02:56:23,454 adding 'MDAnalysis/topology/MinimalParser.py' 2023-08-29T02:56:23,457 adding 'MDAnalysis/topology/PDBParser.py' 2023-08-29T02:56:23,458 adding 'MDAnalysis/topology/PDBQTParser.py' 2023-08-29T02:56:23,460 adding 'MDAnalysis/topology/PQRParser.py' 2023-08-29T02:56:23,462 adding 'MDAnalysis/topology/PSFParser.py' 2023-08-29T02:56:23,464 adding 'MDAnalysis/topology/ParmEdParser.py' 2023-08-29T02:56:23,467 adding 'MDAnalysis/topology/TOPParser.py' 2023-08-29T02:56:23,469 adding 'MDAnalysis/topology/TPRParser.py' 2023-08-29T02:56:23,471 adding 'MDAnalysis/topology/TXYZParser.py' 2023-08-29T02:56:23,472 adding 'MDAnalysis/topology/XYZParser.py' 2023-08-29T02:56:23,474 adding 'MDAnalysis/topology/__init__.py' 2023-08-29T02:56:23,476 adding 'MDAnalysis/topology/base.py' 2023-08-29T02:56:23,478 adding 'MDAnalysis/topology/core.py' 2023-08-29T02:56:23,480 adding 'MDAnalysis/topology/guessers.py' 2023-08-29T02:56:23,482 adding 'MDAnalysis/topology/tables.py' 2023-08-29T02:56:23,484 adding 'MDAnalysis/topology/tpr/__init__.py' 2023-08-29T02:56:23,486 adding 'MDAnalysis/topology/tpr/obj.py' 2023-08-29T02:56:23,488 adding 'MDAnalysis/topology/tpr/setting.py' 2023-08-29T02:56:23,492 adding 'MDAnalysis/topology/tpr/utils.py' 2023-08-29T02:56:23,494 adding 'MDAnalysis/transformations/__init__.py' 2023-08-29T02:56:23,496 adding 'MDAnalysis/transformations/base.py' 2023-08-29T02:56:23,497 adding 'MDAnalysis/transformations/boxdimensions.py' 2023-08-29T02:56:23,499 adding 'MDAnalysis/transformations/fit.py' 2023-08-29T02:56:23,501 adding 'MDAnalysis/transformations/nojump.py' 2023-08-29T02:56:23,502 adding 'MDAnalysis/transformations/positionaveraging.py' 2023-08-29T02:56:23,504 adding 'MDAnalysis/transformations/rotate.py' 2023-08-29T02:56:23,506 adding 'MDAnalysis/transformations/translate.py' 2023-08-29T02:56:23,507 adding 'MDAnalysis/transformations/wrap.py' 2023-08-29T02:56:23,509 adding 'MDAnalysis/visualization/__init__.py' 2023-08-29T02:56:23,512 adding 'MDAnalysis/visualization/streamlines.py' 2023-08-29T02:56:23,515 adding 'MDAnalysis/visualization/streamlines_3D.py' 2023-08-29T02:56:23,518 adding 'MDAnalysis-2.6.1.dist-info/AUTHORS' 2023-08-29T02:56:23,522 adding 'MDAnalysis-2.6.1.dist-info/LICENSE' 2023-08-29T02:56:23,527 adding 'MDAnalysis-2.6.1.dist-info/METADATA' 2023-08-29T02:56:23,528 adding 'MDAnalysis-2.6.1.dist-info/WHEEL' 2023-08-29T02:56:23,529 adding 'MDAnalysis-2.6.1.dist-info/top_level.txt' 2023-08-29T02:56:23,533 adding 'MDAnalysis-2.6.1.dist-info/RECORD' 2023-08-29T02:56:23,646 removing build/bdist.linux-armv7l/wheel 2023-08-29T02:56:23,923 Building wheel for mdanalysis (pyproject.toml): finished with status 'done' 2023-08-29T02:56:24,135 Created wheel for mdanalysis: filename=MDAnalysis-2.6.1-cp39-cp39-linux_armv7l.whl size=9108719 sha256=00c43ef1479c539475a06a2e034c1c76c8d128876384a8a1a6ed9dd4c47c2670 2023-08-29T02:56:24,136 Stored in directory: /tmp/pip-ephem-wheel-cache-3m4rmdk9/wheels/85/2d/3e/0340565be58533b13e003d790852e6dd3044fd931951e164df 2023-08-29T02:56:24,164 Successfully built mdanalysis 2023-08-29T02:56:24,413 Removed build tracker: '/tmp/pip-build-tracker-9kxkbgp7'