2024-05-30T17:29:29,721 Created temporary directory: /tmp/pip-build-tracker-n4ag0wfq 2024-05-30T17:29:29,723 Initialized build tracking at /tmp/pip-build-tracker-n4ag0wfq 2024-05-30T17:29:29,723 Created build tracker: /tmp/pip-build-tracker-n4ag0wfq 2024-05-30T17:29:29,723 Entered build tracker: /tmp/pip-build-tracker-n4ag0wfq 2024-05-30T17:29:29,724 Created temporary directory: /tmp/pip-wheel-z13py9o_ 2024-05-30T17:29:29,728 Created temporary directory: /tmp/pip-ephem-wheel-cache-krm7yxf7 2024-05-30T17:29:29,752 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-30T17:29:29,755 2 location(s) to search for versions of mdtraj: 2024-05-30T17:29:29,755 * https://pypi.org/simple/mdtraj/ 2024-05-30T17:29:29,755 * https://www.piwheels.org/simple/mdtraj/ 2024-05-30T17:29:29,756 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2024-05-30T17:29:29,757 Getting page https://pypi.org/simple/mdtraj/ 2024-05-30T17:29:29,758 Found index url https://pypi.org/simple/ 2024-05-30T17:29:29,810 Fetched page https://pypi.org/simple/mdtraj/ as application/vnd.pypi.simple.v1+json 2024-05-30T17:29:29,826 Found link https://files.pythonhosted.org/packages/cb/82/93ced2a2e5d37f36330fe3e74081fdd4ce8f933ebd16b4fab14cb5c6c29c/mdtraj-0.3.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.3 2024-05-30T17:29:29,826 Found link https://files.pythonhosted.org/packages/bb/79/e0703632501b528c6d4fb87e672aa68e431579e61ddf15b9178554e45a8e/mdtraj-0.3.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.3.1 2024-05-30T17:29:29,826 Skipping link: unsupported archive format: .exe: https://files.pythonhosted.org/packages/76/8f/0e6b0243ec53f87b024e84b26b0ced2ca716dd347ac459ef5c65e887fd02/mdtraj-0.3.1.win-amd64-py2.7.exe (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,827 Found link https://files.pythonhosted.org/packages/6e/2c/5e68a951b1d038ce32d5e0e128f56ee7ff0ea0ce933e7c05a2b9a2c56b9d/mdtraj-0.4.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.4.0 2024-05-30T17:29:29,827 Found link https://files.pythonhosted.org/packages/83/4d/820da3023ad7d89e3dfcdfca11a298ded20d99383f43ce2bdef30c120d8e/mdtraj-0.4.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.4.1 2024-05-30T17:29:29,827 Found link https://files.pythonhosted.org/packages/c3/6d/3c211650aacc169d271d86de954d08f96b835e7f0d08de472cf7fe5b41b3/mdtraj-0.4.3.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.4.3 2024-05-30T17:29:29,827 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/d7/ad/6610b9029c85be5fe896b9a6d0bd6a7e960db1ec751ff7e6a36594eebd05/mdtraj-0.4.3.win32-py2.6.msi (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,828 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/f2/d0/2ea0d56c38693e121a8b646a688cbb3f7d1d5d5dc3a89893e358e70cf4e3/mdtraj-0.4.3.win32-py2.7.msi (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,828 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/c5/fa/7f4579a0eb11ea6eab4cf94a0b10ca9bebdeeee53e022ad7a66d7a3c5dfb/mdtraj-0.4.3.win32-py3.2.msi (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,828 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/28/e5/cb27f0a2b7a3c604704fe9fa92d8b3f5e82bd3a5a50f17548d79875618d7/mdtraj-0.4.3.win32-py3.3.msi (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,828 Found link https://files.pythonhosted.org/packages/e5/88/d95a7bf9ab9f170c4a765b24aef3249f8b48419eb8200c0e6e0cefb8df27/mdtraj-0.4.3.zip (from https://pypi.org/simple/mdtraj/), version: 0.4.3 2024-05-30T17:29:29,828 Found link https://files.pythonhosted.org/packages/d7/77/493f388512cb4e90e787ed60e206b053c4999f59ea8e473f182c041e7bb5/mdtraj-0.5.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.5.0 2024-05-30T17:29:29,829 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/0e/5a/a74bf3100d9fa5ff67cf6b271c8ad0254402f96f68da5b4015bdd62313fd/mdtraj-0.5.0.win32-py2.7.msi (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,829 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/58/b4/71dae8ecfac23b90e0bbcbcb21bc3770277d42717e7476cc6502b07a2b35/mdtraj-0.5.0.win32-py3.2.msi (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,829 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/16/bc/e7b082171abfe965d04cfafd5851541644c0cb831a6a2a24167986cd1fe1/mdtraj-0.5.0.win32-py3.3.msi (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,829 Found link https://files.pythonhosted.org/packages/f3/91/344c3301a96d586b7280b9fcc70c59a804df499219f0fbb750c8b2bfb818/mdtraj-0.5.0.zip (from https://pypi.org/simple/mdtraj/), version: 0.5.0 2024-05-30T17:29:29,830 Found link https://files.pythonhosted.org/packages/0f/d3/df89fa19d0572c58f82e17d57a1409cefb7525b0c96930876f42563bc937/mdtraj-0.5.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.5.1 2024-05-30T17:29:29,830 Found link https://files.pythonhosted.org/packages/07/17/04c7422cc1092ca74b51da1f9ba4f76e38b53ef6f35bf4ad4bb65301c316/mdtraj-0.5.1.zip (from https://pypi.org/simple/mdtraj/), version: 0.5.1 2024-05-30T17:29:29,830 Found link https://files.pythonhosted.org/packages/59/41/0768b99fcb72f568950c767a0866b92d9a328f9b3c848e3f0f6426c49bc7/mdtraj-0.6.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.6.0 2024-05-30T17:29:29,830 Found link https://files.pythonhosted.org/packages/85/33/c0708f41cc090a886342325cb99db876b555a181ee18a3a1086b1b87dfd1/mdtraj-0.6.0.zip (from https://pypi.org/simple/mdtraj/), version: 0.6.0 2024-05-30T17:29:29,831 Found link https://files.pythonhosted.org/packages/b1/b4/6219cf2656a223f06d3e40d5098fa186aba73ac5d3cbb08348fa73bf0c7e/mdtraj-0.6.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.6.1 2024-05-30T17:29:29,831 Found link https://files.pythonhosted.org/packages/59/3e/3184bc16bbf5f14ea3148552ae43ebfb28e3abc6ea08a76e3e31b81f938a/mdtraj-0.6.1.zip (from https://pypi.org/simple/mdtraj/), version: 0.6.1 2024-05-30T17:29:29,831 Found link https://files.pythonhosted.org/packages/2d/7b/67e57aeabcd1383fac5d169f866836e00410a41f6311d4c3e1d809a9c9e8/mdtraj-0.7.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.7.0 2024-05-30T17:29:29,832 Found link https://files.pythonhosted.org/packages/bb/31/a472847da32caa824a73c3794f5816005b2a213f6c35df20dc55d1d07be8/mdtraj-0.7.0.zip (from https://pypi.org/simple/mdtraj/), version: 0.7.0 2024-05-30T17:29:29,832 Found link https://files.pythonhosted.org/packages/3a/f1/de324881e0c838b8eda4222a02ac5b0595e52c40225046a67e845db5fb35/mdtraj-0.8.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.8.0 2024-05-30T17:29:29,832 Found link https://files.pythonhosted.org/packages/d8/87/01f61e5cabbf391ed20ec15854454f7bd76d752413be983654c2de738292/mdtraj-0.8.0.zip (from https://pypi.org/simple/mdtraj/), version: 0.8.0 2024-05-30T17:29:29,832 Found link https://files.pythonhosted.org/packages/77/72/4f559e05820f485e2f1542154660ed9746e4822a097022ab79a5afba53a1/mdtraj-0.9.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.9.0 2024-05-30T17:29:29,833 Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/48/71/d6bf7c8e7fa50e826a16c89bf00aa636953aa6efa462d01f04543f51536d/mdtraj-0.9.0.win32-py2.7.msi (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,833 Found link https://files.pythonhosted.org/packages/5a/a4/ab877500acc0e0b953d8ffa8de21719fcbb78749c2fd682f82601a0f3a3d/mdtraj-0.9.0.zip (from https://pypi.org/simple/mdtraj/), version: 0.9.0 2024-05-30T17:29:29,833 Found link https://files.pythonhosted.org/packages/de/4b/cb27df1a4b50e52cbbd33d8e123d3f252e108a263a8389a8297e5810b453/mdtraj-1.0.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.0.0 2024-05-30T17:29:29,833 Found link https://files.pythonhosted.org/packages/8e/36/9fd92ca45c2b84384f78020524edb9dfd2d4cefc0595472cc60b64af62ed/mdtraj-1.0.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.0.0 2024-05-30T17:29:29,834 Found link https://files.pythonhosted.org/packages/dd/e2/b7a137d7bff0dba7347d3ad2462e811bdcfc8de0bc3f6b78f93c2af78a58/mdtraj-1.1.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.1.0 2024-05-30T17:29:29,834 Found link https://files.pythonhosted.org/packages/13/c2/b758f772bbf35fe8069509d59c701de491f2cf3c9b63658e4ddc3cfcf468/mdtraj-1.1.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.1.0 2024-05-30T17:29:29,834 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/1e/bc/4d4fd31a09fbed9d2e1e6a90fa0657e5c22f40b9ae542f932854b20b867a/mdtraj-1.2.0-cp27-none-win32.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,834 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/59/d7/f4809991e14a568656957523111763cd3105ad3f63d53b470643f3c391c7/mdtraj-1.2.0-cp33-none-win32.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,835 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/47/ec/0da56abb0793e6c03ca647bb66a01e175e9cd80623b77cc3eee7aa4b0169/mdtraj-1.2.0-cp34-none-win32.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,835 Found link https://files.pythonhosted.org/packages/b9/7d/a2878b6c3da5e04ad15f906235bbf6507d5b801465b6a7626cd7f6e33289/mdtraj-1.2.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.2.0 2024-05-30T17:29:29,835 Found link https://files.pythonhosted.org/packages/ad/60/131151a1dacdf1fb8aa2afb20d2f7865802ee8a654f5c46bf0990cd44b77/mdtraj-1.2.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.2.0 2024-05-30T17:29:29,835 Found link https://files.pythonhosted.org/packages/19/43/14b0d39a19b9bf7129c1d1c00fb3ef6b201dd6ca26d4b5d82e06d5523931/mdtraj-1.3.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.3.0 2024-05-30T17:29:29,836 Found link https://files.pythonhosted.org/packages/52/1c/5241b6d7eedc4d1c17a5b87665216f5781efdd7b3ad742fec151ca5db5f8/mdtraj-1.3.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.3.0 2024-05-30T17:29:29,836 Found link https://files.pythonhosted.org/packages/97/1c/bce6eb773069063889ddf3969cdbd547697cca8909de4a285721bd4b936c/mdtraj-1.4.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.4.0 2024-05-30T17:29:29,836 Found link https://files.pythonhosted.org/packages/20/4d/0fdff16d6d1b9a1e1e0d6f0391226c2a0791810e07772fa7e3b6713e5c9a/mdtraj-1.4.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.4.0 2024-05-30T17:29:29,836 Found link https://files.pythonhosted.org/packages/37/bb/c7261dd1fc35105898af6de578719e8eb18aa33f70dd38a4257ff68118c4/mdtraj-1.4.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.4.1 2024-05-30T17:29:29,837 Found link https://files.pythonhosted.org/packages/eb/b4/4fd2c5d63e4a1f10047df8a3f83071d41ba9203abf1a86d381f2c16cef94/mdtraj-1.4.1.zip (from https://pypi.org/simple/mdtraj/), version: 1.4.1 2024-05-30T17:29:29,837 Found link https://files.pythonhosted.org/packages/af/43/7594de45f455b32c5a057bc323336461a7f4299a5e93dfb57038e0c7c99c/mdtraj-1.4.2.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.4.2 2024-05-30T17:29:29,837 Found link https://files.pythonhosted.org/packages/79/d7/7ec8477e4293f027acd7695ae8d493eb7985aec5666ce3d117d48794fa5c/mdtraj-1.4.2.zip (from https://pypi.org/simple/mdtraj/), version: 1.4.2 2024-05-30T17:29:29,837 Found link https://files.pythonhosted.org/packages/f8/36/a0a83efc5f48db485bdefd15a7ade8a80876bbe178318cfa14ced3cb0c87/mdtraj-1.5.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.5.0 2024-05-30T17:29:29,838 Found link https://files.pythonhosted.org/packages/b2/2c/1cfc1f7879ea82293afca1edd595f3ca39e25f8411627175e88ea6819f83/mdtraj-1.5.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.5.0 2024-05-30T17:29:29,838 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/a8/24/4c267bc9753b3d1218b1d9c9220d3811d71eea2cfba590f512bcbb2a9c3b/mdtraj-1.5.1-cp27-none-macosx_10_5_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,838 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/5e/07/f6d8703864e39672cb420701e6a8ef0c2d3000e9b0bcc25777d29d526350/mdtraj-1.5.1-cp34-cp34m-macosx_10_5_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,838 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/2b/6e/a791501a9a60b3cb2063fc3db8d4d9b1a27cfa4432261b98f804f9bf34e1/mdtraj-1.5.1-cp35-cp35m-macosx_10_5_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,839 Found link https://files.pythonhosted.org/packages/dc/6c/2173608f090cf361b8c858e7db974757a8ec9c639ce69b100e9a4608875e/mdtraj-1.5.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.5.1 2024-05-30T17:29:29,839 Found link https://files.pythonhosted.org/packages/78/ae/82df7eca71fa9e71ad4638f8c222164ccc3583874cb4a6875a04586312bc/mdtraj-1.5.1.zip (from https://pypi.org/simple/mdtraj/), version: 1.5.1 2024-05-30T17:29:29,839 Found link https://files.pythonhosted.org/packages/40/21/40aeb64c81f480e07b1e1c31c6b3b332bc38df08d5fd30210fc235acdb3d/mdtraj-1.6.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.6.0 2024-05-30T17:29:29,839 Found link https://files.pythonhosted.org/packages/8f/9e/cf5814ce6a29a474dc2b61492ed36dde1397b1707e63248bafe495529c29/mdtraj-1.6.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.6.0 2024-05-30T17:29:29,840 Found link https://files.pythonhosted.org/packages/a7/09/abb145901e09665d3a7931527e34a160049cebf4eba3506a69db2093f5f9/mdtraj-1.6.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.6.1 2024-05-30T17:29:29,840 Found link https://files.pythonhosted.org/packages/38/44/179f101e32ab7ceb52864fb4ef2955c0807b9f548c087f39f2cfd18cb498/mdtraj-1.6.1.zip (from https://pypi.org/simple/mdtraj/), version: 1.6.1 2024-05-30T17:29:29,840 Found link https://files.pythonhosted.org/packages/bf/81/6f611041374bd7d2d49a15040d999cc52eed1a44e856a4a8d9c02370ac37/mdtraj-1.7.2.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.7.2 2024-05-30T17:29:29,840 Found link https://files.pythonhosted.org/packages/ff/b2/8785a8c9c7119e1a7c4e64072ccf428f75a3b0a9782a7ac25e5402b0a59d/mdtraj-1.7.2.zip (from https://pypi.org/simple/mdtraj/), version: 1.7.2 2024-05-30T17:29:29,841 Found link https://files.pythonhosted.org/packages/cd/9f/027fa58d4e93dd3d700e22d5766961c970f6882c2bffd33daef55219d078/mdtraj-1.8.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.8.0 2024-05-30T17:29:29,841 Found link https://files.pythonhosted.org/packages/4a/2e/5bb01aaa8cd2ea9d75dd2ac12fd9f04f7137a8c996bde0138ad1b5e54ecb/mdtraj-1.8.0.zip (from https://pypi.org/simple/mdtraj/), version: 1.8.0 2024-05-30T17:29:29,841 Found link https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.1 2024-05-30T17:29:29,841 Found link https://files.pythonhosted.org/packages/e0/9e/857f613eae8af3fb8cc73904b3edf622c58de3884c5989e4466973c3c9ee/mdtraj-1.9.2.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.2 2024-05-30T17:29:29,842 Found link https://files.pythonhosted.org/packages/72/68/1efc74927df6fdaaa4816556a2534f4560cb69ed573ccac728e4fb8e3e09/mdtraj-1.9.3.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.3 2024-05-30T17:29:29,842 Found link https://files.pythonhosted.org/packages/50/1d/581a080a1900f61bb1c0388e29517a54d4034faa094d40d794e1f96597d9/mdtraj-1.9.4.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.4 2024-05-30T17:29:29,842 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/1b/77/3ac1597812fc28964662587d405f85986206192623b434f7d0fa1b4a6a5b/mdtraj-1.9.5-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,842 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/af/da/271e93bb98bc93ccac17bc1f31f814be4f9e7024ac19bf31af892a462030/mdtraj-1.9.5-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,843 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/3b/fd/4ffba665d0b0346072f61d0e8ef7ab281202db445d99136c717c89169a97/mdtraj-1.9.5-cp38-cp38-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,843 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/68/53/2f666107565f4735abd859b6af6867353eb08d0e9728d90fb0abc12d578e/mdtraj-1.9.5-cp39-cp39-manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,843 Found link https://files.pythonhosted.org/packages/d8/cb/5dcc31c7e2c4485bd2aea66233def28954f2dc530607f5c43fefab71a963/mdtraj-1.9.5.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.5 2024-05-30T17:29:29,843 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/fe/a7/2a1392fe56ddd22a9cf5dcff7d684bdd7ce146d5c32839080dd8de7122dd/mdtraj-1.9.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,844 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/ce/ee/2015ff88cacb7c75b5e1cf6a57e8a089549b0e76bcd9474a08845f7ef12f/mdtraj-1.9.6-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,844 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/c0/61/2fb002b9b2ab90567eb1a837ed510152ddadd5b8358ac800b591e37675e0/mdtraj-1.9.6-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,844 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/09/49/85dc22a3c28108dfd0bce8a4268ae3937167b18fac531a0d801505cad7d9/mdtraj-1.9.6-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,844 Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.6 2024-05-30T17:29:29,844 Found link https://files.pythonhosted.org/packages/2f/03/c174bfb6471f796472ce1d8695f6c0d1a20ad6516cb789b70052df45b7a6/mdtraj-1.9.7.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.7 2024-05-30T17:29:29,845 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/5d/1c/75a4c0ec4fb42e5daafaf13a49c03194f76b7deb0134d894a5004d833446/mdtraj-1.9.8-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,845 Found link https://files.pythonhosted.org/packages/53/02/a30f67a8bd3dba6d6e4ecc02bee290f425bf30c504a8a959a04e2be321ac/mdtraj-1.9.8.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.8 2024-05-30T17:29:29,845 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/88/12/ecbe28c87bc3df8c4880cc742923a6f40633ca076c8f44b03533dfce0b66/mdtraj-1.9.9-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2024-05-30T17:29:29,845 Found link https://files.pythonhosted.org/packages/0b/45/f94a06c8a3b1f91a692637f5216951b2205a265166ecfb1c7e3f4e172200/mdtraj-1.9.9.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.9.9 2024-05-30T17:29:29,846 Found link https://files.pythonhosted.org/packages/11/b7/e1ecec12743be0e295395c0cdb763666c1b01be989942cb9f6e4c89f19a1/mdtraj-1.10.0rc1.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.10.0rc1 2024-05-30T17:29:29,846 Found link https://files.pythonhosted.org/packages/da/fd/4bd7942b380e206b74fd74e2861425332077f34fd7946bc29ce40fea46c4/mdtraj-1.10.0rc2.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.10.0rc2 2024-05-30T17:29:29,846 Found link https://files.pythonhosted.org/packages/5a/a0/645d6a0156a982c410f61533d96cdb9c5086f0ac55ea97be1fc87a7d95f6/mdtraj-1.10.0.tar.gz (from https://pypi.org/simple/mdtraj/), version: 1.10.0 2024-05-30T17:29:29,847 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2024-05-30T17:29:29,847 Getting page https://www.piwheels.org/simple/mdtraj/ 2024-05-30T17:29:29,848 Found index url https://www.piwheels.org/simple/ 2024-05-30T17:29:30,030 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2024-05-30T17:29:30,037 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp311-cp311-linux_armv6l.whl#sha256=b303bd85a6fe8b1a38c95c47fe66624944c9783bcccb08afdc041d048d4a489b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,038 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp311-cp311-linux_armv7l.whl#sha256=b303bd85a6fe8b1a38c95c47fe66624944c9783bcccb08afdc041d048d4a489b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,038 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp37-cp37m-linux_armv6l.whl#sha256=1f004eae3fa9fdf88cbe94eb85a14d097452e4c35a5e57a695cd836a33e38fd5 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,038 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp37-cp37m-linux_armv7l.whl#sha256=1f004eae3fa9fdf88cbe94eb85a14d097452e4c35a5e57a695cd836a33e38fd5 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,038 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp311-cp311-linux_armv6l.whl#sha256=bb4a20fe32bcfb564d4efcd3c10b2d6c88728eecacf8bd1b53dd402e387c444f (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,039 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp311-cp311-linux_armv7l.whl#sha256=bb4a20fe32bcfb564d4efcd3c10b2d6c88728eecacf8bd1b53dd402e387c444f (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,039 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp37-cp37m-linux_armv6l.whl#sha256=cb090c5366b7b76d938daa16ca5a431a4fe751344ec320479b3ba8134a6ff4bd (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,039 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp37-cp37m-linux_armv7l.whl#sha256=cb090c5366b7b76d938daa16ca5a431a4fe751344ec320479b3ba8134a6ff4bd (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,039 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv6l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,039 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv7l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,040 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp37-cp37m-linux_armv6l.whl#sha256=355ab9108c6d079032d3b97eaa3ad76e261893dcd45a07b62c5e8a493600e06d (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,040 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp37-cp37m-linux_armv7l.whl#sha256=355ab9108c6d079032d3b97eaa3ad76e261893dcd45a07b62c5e8a493600e06d (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,040 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv6l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,040 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,040 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv6l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,041 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,041 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv6l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,041 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv7l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,041 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv6l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,041 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,042 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv6l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,042 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,042 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,042 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv7l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,042 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv6l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,042 Skipping link: No binaries permitted for mdtraj: https://www.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2024-05-30T17:29:30,043 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2024-05-30T17:29:30,043 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2024-05-30T17:29:30,067 Given no hashes to check 1 links for project 'mdtraj': discarding no candidates 2024-05-30T17:29:30,083 Collecting mdtraj==1.10.0 2024-05-30T17:29:30,085 Created temporary directory: /tmp/pip-unpack-n9o1wvi7 2024-05-30T17:29:30,129 Downloading mdtraj-1.10.0.tar.gz (1.8 MB) 2024-05-30T17:29:31,434 Added mdtraj==1.10.0 from https://files.pythonhosted.org/packages/5a/a0/645d6a0156a982c410f61533d96cdb9c5086f0ac55ea97be1fc87a7d95f6/mdtraj-1.10.0.tar.gz to build tracker '/tmp/pip-build-tracker-n4ag0wfq' 2024-05-30T17:29:31,442 Created temporary directory: /tmp/pip-build-env-3nq7ycgc 2024-05-30T17:29:31,452 Installing build dependencies: started 2024-05-30T17:29:31,453 Running command pip subprocess to install build dependencies 2024-05-30T17:29:32,640 Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2024-05-30T17:29:33,156 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-30T17:29:34,617 Collecting setuptools 2024-05-30T17:29:34,634 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.0.0-py3-none-any.whl (863 kB) 2024-05-30T17:29:34,888 Collecting wheel 2024-05-30T17:29:34,905 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-05-30T17:29:35,937 Collecting numpy<2 2024-05-30T17:29:35,955 Using cached https://www.piwheels.org/simple/numpy/numpy-1.26.4-cp39-cp39-linux_armv7l.whl (5.6 MB) 2024-05-30T17:29:36,261 Collecting oldest-supported-numpy 2024-05-30T17:29:36,278 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2023.12.21-py3-none-any.whl (4.9 kB) 2024-05-30T17:29:37,683 Collecting Cython~=0.29.36 2024-05-30T17:29:37,706 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.37-cp39-cp39-linux_armv7l.whl (4.9 MB) 2024-05-30T17:29:38,275 Collecting numpy<2 2024-05-30T17:29:38,292 Using cached https://www.piwheels.org/simple/numpy/numpy-1.19.3-cp39-cp39-linux_armv7l.whl (10.5 MB) 2024-05-30T17:29:40,372 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2024-05-30T17:29:40,596 Creating /tmp/pip-build-env-3nq7ycgc/overlay/bin 2024-05-30T17:29:40,598 changing mode of /tmp/pip-build-env-3nq7ycgc/overlay/bin/wheel to 755 2024-05-30T17:29:49,115 changing mode of /tmp/pip-build-env-3nq7ycgc/overlay/bin/f2py to 755 2024-05-30T17:29:49,118 changing mode of /tmp/pip-build-env-3nq7ycgc/overlay/bin/f2py3 to 755 2024-05-30T17:29:49,120 changing mode of /tmp/pip-build-env-3nq7ycgc/overlay/bin/f2py3.9 to 755 2024-05-30T17:29:51,783 changing mode of /tmp/pip-build-env-3nq7ycgc/overlay/bin/cygdb to 755 2024-05-30T17:29:51,786 changing mode of /tmp/pip-build-env-3nq7ycgc/overlay/bin/cython to 755 2024-05-30T17:29:51,788 changing mode of /tmp/pip-build-env-3nq7ycgc/overlay/bin/cythonize to 755 2024-05-30T17:29:51,834 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. 2024-05-30T17:29:51,834 scipy 1.13.0 requires numpy<2.3,>=1.22.4, but you have numpy 1.19.3 which is incompatible. 2024-05-30T17:29:51,835 Successfully installed Cython-0.29.37 numpy-1.19.3 oldest-supported-numpy-2023.12.21 setuptools-70.0.0 wheel-0.43.0 2024-05-30T17:29:52,491 Installing build dependencies: finished with status 'done' 2024-05-30T17:29:52,501 Getting requirements to build wheel: started 2024-05-30T17:29:52,502 Running command Getting requirements to build wheel 2024-05-30T17:29:53,242 Using built-in specs. 2024-05-30T17:29:53,243 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-30T17:29:53,243 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-30T17:29:53,243 Target: arm-linux-gnueabihf 2024-05-30T17:29:53,243 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-30T17:29:53,243 Thread model: posix 2024-05-30T17:29:53,243 Supported LTO compression algorithms: zlib zstd 2024-05-30T17:29:53,244 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-30T17:29:57,425 C compiler: 2024-05-30T17:29:57,425 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-30T17:29:57,425 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-30T17:29:57,425 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-30T17:29:57,425 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-30T17:29:57,426 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-30T17:29:57,426 running egg_info 2024-05-30T17:29:57,431 writing mdtraj.egg-info/PKG-INFO 2024-05-30T17:29:57,434 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-30T17:29:57,436 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-30T17:29:57,438 writing requirements to mdtraj.egg-info/requires.txt 2024-05-30T17:29:57,439 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-30T17:29:57,480 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-30T17:29:57,501 reading manifest template 'MANIFEST.in' 2024-05-30T17:29:58,091 no previously-included directories found matching '__pycache__' 2024-05-30T17:29:58,092 no previously-included directories found matching '*.pyc' 2024-05-30T17:29:58,093 adding license file 'LICENSE' 2024-05-30T17:29:58,106 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-30T17:29:58,191 Getting requirements to build wheel: finished with status 'done' 2024-05-30T17:29:58,200 Created temporary directory: /tmp/pip-modern-metadata-0k9r5nl2 2024-05-30T17:29:58,205 Preparing metadata (pyproject.toml): started 2024-05-30T17:29:58,206 Running command Preparing metadata (pyproject.toml) 2024-05-30T17:29:58,887 Using built-in specs. 2024-05-30T17:29:58,888 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-30T17:29:58,888 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-30T17:29:58,888 Target: arm-linux-gnueabihf 2024-05-30T17:29:58,888 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-30T17:29:58,888 Thread model: posix 2024-05-30T17:29:58,888 Supported LTO compression algorithms: zlib zstd 2024-05-30T17:29:58,889 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-30T17:30:02,857 /tmp/pip-wheel-z13py9o_/mdtraj_6754c22392964e6cb16387cfd23e2100/basesetup.py:518: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-0k9r5nl2 --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2024-05-30T17:30:02,857 warnings.warn( 2024-05-30T17:30:04,813 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-30T17:30:04,814 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-30T17:30:04,814 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-30T17:30:31,075 C compiler: 2024-05-30T17:30:31,076 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-30T17:30:31,076 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-30T17:30:31,076 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-30T17:30:31,076 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-30T17:30:31,077 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-30T17:30:31,077 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-30T17:30:31,077 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-30T17:30:31,077 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-30T17:30:31,077 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-30T17:30:31,077 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-30T17:30:31,077 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-30T17:30:31,077 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-30T17:30:31,078 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-30T17:30:31,078 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-30T17:30:31,078 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-30T17:30:31,180 running dist_info 2024-05-30T17:30:31,187 creating /tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info 2024-05-30T17:30:31,194 writing /tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info/PKG-INFO 2024-05-30T17:30:31,198 writing dependency_links to /tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info/dependency_links.txt 2024-05-30T17:30:31,199 writing entry points to /tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info/entry_points.txt 2024-05-30T17:30:31,201 writing requirements to /tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info/requires.txt 2024-05-30T17:30:31,202 writing top-level names to /tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info/top_level.txt 2024-05-30T17:30:31,203 writing manifest file '/tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info/SOURCES.txt' 2024-05-30T17:30:31,254 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,254 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,255 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,255 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,255 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,255 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,255 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,255 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,256 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,256 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,257 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,257 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:30:31,271 reading manifest file '/tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info/SOURCES.txt' 2024-05-30T17:30:31,273 reading manifest template 'MANIFEST.in' 2024-05-30T17:30:31,834 no previously-included directories found matching '__pycache__' 2024-05-30T17:30:31,835 no previously-included directories found matching '*.pyc' 2024-05-30T17:30:31,835 adding license file 'LICENSE' 2024-05-30T17:30:31,847 writing manifest file '/tmp/pip-modern-metadata-0k9r5nl2/mdtraj.egg-info/SOURCES.txt' 2024-05-30T17:30:31,848 creating '/tmp/pip-modern-metadata-0k9r5nl2/mdtraj-1.10.0.dist-info' 2024-05-30T17:30:32,639 Preparing metadata (pyproject.toml): finished with status 'done' 2024-05-30T17:30:32,645 Source in /tmp/pip-wheel-z13py9o_/mdtraj_6754c22392964e6cb16387cfd23e2100 has version 1.10.0, which satisfies requirement mdtraj==1.10.0 from https://files.pythonhosted.org/packages/5a/a0/645d6a0156a982c410f61533d96cdb9c5086f0ac55ea97be1fc87a7d95f6/mdtraj-1.10.0.tar.gz 2024-05-30T17:30:32,646 Removed mdtraj==1.10.0 from https://files.pythonhosted.org/packages/5a/a0/645d6a0156a982c410f61533d96cdb9c5086f0ac55ea97be1fc87a7d95f6/mdtraj-1.10.0.tar.gz from build tracker '/tmp/pip-build-tracker-n4ag0wfq' 2024-05-30T17:30:32,650 Created temporary directory: /tmp/pip-unpack-2wtkwh_e 2024-05-30T17:30:32,651 Created temporary directory: /tmp/pip-unpack-l7z9ejs7 2024-05-30T17:30:32,660 Building wheels for collected packages: mdtraj 2024-05-30T17:30:32,664 Created temporary directory: /tmp/pip-wheel-m55eg420 2024-05-30T17:30:32,664 Destination directory: /tmp/pip-wheel-m55eg420 2024-05-30T17:30:32,666 Building wheel for mdtraj (pyproject.toml): started 2024-05-30T17:30:32,667 Running command Building wheel for mdtraj (pyproject.toml) 2024-05-30T17:30:33,356 Using built-in specs. 2024-05-30T17:30:33,357 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2024-05-30T17:30:33,357 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper 2024-05-30T17:30:33,357 Target: arm-linux-gnueabihf 2024-05-30T17:30:33,357 Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2024-05-30T17:30:33,357 Thread model: posix 2024-05-30T17:30:33,357 Supported LTO compression algorithms: zlib zstd 2024-05-30T17:30:33,357 gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1) 2024-05-30T17:30:38,998 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-30T17:30:38,998 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-30T17:30:38,998 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2024-05-30T17:31:02,576 C compiler: 2024-05-30T17:31:02,577 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2024-05-30T17:31:02,577 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2024-05-30T17:31:02,577 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2024-05-30T17:31:02,577 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2024-05-30T17:31:02,577 Attempting to autodetect NEON support... Did not detect NEON support 2024-05-30T17:31:02,578 [ 1/10] Cythonizing mdtraj/formats/dcd/dcd.pyx 2024-05-30T17:31:02,578 [ 2/10] Cythonizing mdtraj/geometry/drid.pyx 2024-05-30T17:31:02,578 [ 3/10] Cythonizing mdtraj/geometry/neighborlist.pyx 2024-05-30T17:31:02,578 [ 4/10] Cythonizing mdtraj/geometry/neighbors.pyx 2024-05-30T17:31:02,578 [ 5/10] Cythonizing mdtraj/geometry/src/_geometry.pyx 2024-05-30T17:31:02,578 [ 6/10] Cythonizing mdtraj/rmsd/_lprmsd.pyx 2024-05-30T17:31:02,578 [ 7/10] Cythonizing mdtraj/formats/dtr/dtr.pyx 2024-05-30T17:31:02,579 [ 8/10] Cythonizing mdtraj/formats/xtc/trr.pyx 2024-05-30T17:31:02,579 [ 9/10] Cythonizing mdtraj/formats/xtc/xtc.pyx 2024-05-30T17:31:02,579 [10/10] Cythonizing mdtraj/rmsd/_rmsd.pyx 2024-05-30T17:31:02,702 running bdist_wheel 2024-05-30T17:31:02,742 running build 2024-05-30T17:31:02,742 running build_py 2024-05-30T17:31:02,755 creating build 2024-05-30T17:31:02,756 creating build/lib.linux-armv7l-cpython-39 2024-05-30T17:31:02,757 creating build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-30T17:31:02,758 copying mdtraj/io.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-30T17:31:02,760 copying mdtraj/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-30T17:31:02,762 copying mdtraj/version.py -> build/lib.linux-armv7l-cpython-39/mdtraj 2024-05-30T17:31:02,764 creating build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-30T17:31:02,765 copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-30T17:31:02,768 copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-30T17:31:02,770 copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/nmr 2024-05-30T17:31:02,773 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,774 copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,776 copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,778 copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,780 copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,782 copying mdtraj/formats/pdbx.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,785 copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,788 copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,791 copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,793 copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,796 copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,798 copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,801 copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,803 copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,806 copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,808 copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,810 copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,813 copying mdtraj/formats/gsd.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,815 copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,818 creating build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,819 copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,822 copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,824 copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,825 copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,827 copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,830 copying mdtraj/geometry/shape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,832 copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,834 copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,836 copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,838 copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,840 copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,842 copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,845 copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,846 copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,849 copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:31:02,852 creating build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-30T17:31:02,852 copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-30T17:31:02,854 copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-30T17:31:02,856 copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-30T17:31:02,859 copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-cpython-39/mdtraj/testing 2024-05-30T17:31:02,862 creating build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-30T17:31:02,863 copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-30T17:31:02,865 copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-30T17:31:02,866 copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-39/mdtraj/scripts 2024-05-30T17:31:02,870 creating build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-30T17:31:02,871 copying mdtraj/core/selection.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-30T17:31:02,873 copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-30T17:31:02,876 copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-30T17:31:02,877 copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-30T17:31:02,881 copying mdtraj/core/topology.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-30T17:31:02,884 copying mdtraj/core/element.py -> build/lib.linux-armv7l-cpython-39/mdtraj/core 2024-05-30T17:31:02,888 creating build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-30T17:31:02,889 copying mdtraj/reporters/xtcreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-30T17:31:02,891 copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-30T17:31:02,893 copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-30T17:31:02,894 copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-30T17:31:02,896 copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-30T17:31:02,898 copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-39/mdtraj/reporters 2024-05-30T17:31:02,901 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,902 copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,904 copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,906 copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,908 copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,910 copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,912 copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,914 copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,916 copying mdtraj/utils/singleton.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils 2024-05-30T17:31:02,919 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-30T17:31:02,920 copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-30T17:31:02,923 copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-30T17:31:02,926 copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb 2024-05-30T17:31:02,928 creating build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,929 copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,931 copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,933 copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,935 copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,937 copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,939 copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,942 copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,944 copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,947 copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,949 copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,951 copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,954 copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,956 copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit 2024-05-30T17:31:02,963 creating build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-30T17:31:02,964 copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-30T17:31:02,967 copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data 2024-05-30T17:31:02,977 running build_ext 2024-05-30T17:31:02,980 building 'mdtraj.formats.xtc' extension 2024-05-30T17:31:02,981 creating build/temp.linux-armv7l-cpython-39 2024-05-30T17:31:02,982 creating build/temp.linux-armv7l-cpython-39/mdtraj 2024-05-30T17:31:02,982 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats 2024-05-30T17:31:02,983 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc 2024-05-30T17:31:02,983 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src 2024-05-30T17:31:02,985 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 -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:03,113 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 -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:03,253 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-30T17:31:03,254 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:03,254 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-30T17:31:03,254 | ^~~~~~ 2024-05-30T17:31:03,255 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:03,255 785 | int smallidx, minidx, maxidx; 2024-05-30T17:31:03,255 | ^~~~~~ 2024-05-30T17:31:03,262 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-30T17:31:03,263 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:03,263 1016 | int errval=1; 2024-05-30T17:31:03,263 | ^~~~~~ 2024-05-30T17:31:03,268 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-30T17:31:03,269 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:03,269 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-30T17:31:03,269 | ^~~~~~ 2024-05-30T17:31:03,270 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:03,270 1302 | int smallidx, minidx, maxidx; 2024-05-30T17:31:03,270 | ^~~~~~ 2024-05-30T17:31:03,279 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-30T17:31:03,280 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:03,280 1509 | int errval=1; 2024-05-30T17:31:03,280 | ^~~~~~ 2024-05-30T17:31:05,397 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 -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:05,477 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’: 2024-05-30T17:31:05,477 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable] 2024-05-30T17:31:05,477 66 | int i,j,result; 2024-05-30T17:31:05,477 | ^ 2024-05-30T17:31:05,477 mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable] 2024-05-30T17:31:05,478 66 | int i,j,result; 2024-05-30T17:31:05,478 | ^ 2024-05-30T17:31:05,478 mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’: 2024-05-30T17:31:05,479 mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2024-05-30T17:31:05,479 119 | if (NULL == xd) 2024-05-30T17:31:05,479 | ^~ 2024-05-30T17:31:05,479 mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2024-05-30T17:31:05,479 122 | do { 2024-05-30T17:31:05,480 | ^~ 2024-05-30T17:31:05,619 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 -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/xtc.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:05,942 In file included from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-30T17:31:05,943 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T17:31:05,943 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-30T17:31:05,943 from mdtraj/formats/xtc/xtc.c:781: 2024-05-30T17:31:05,943 /tmp/pip-build-env-3nq7ycgc/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] 2024-05-30T17:31:05,943 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T17:31:05,943 | ^~~~~~~ 2024-05-30T17:31:12,423 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’: 2024-05-30T17:31:12,423 mdtraj/formats/xtc/xtc.c:693:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:12,424 693 | #define PyInt_FromLong PyLong_FromLong 2024-05-30T17:31:12,424 | ^~~~~~~~~~~~~~~ 2024-05-30T17:31:12,429 mdtraj/formats/xtc/xtc.c:9547:7: note: ‘__pyx_v_status’ was declared here 2024-05-30T17:31:12,429 9547 | int __pyx_v_status; 2024-05-30T17:31:12,429 | ^~~~~~~~~~~~~~ 2024-05-30T17:31:21,834 mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_12_read’: 2024-05-30T17:31:21,839 mdtraj/formats/xtc/xtc.c:8066:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,839 8066 | } else if (unlikely(__pyx_t_39 >= __pyx_pybuffernd_xyz_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-30T17:31:21,839 | ^ 2024-05-30T17:31:21,844 mdtraj/formats/xtc/xtc.c:8062:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,844 8062 | } else if (unlikely(__pyx_t_38 >= __pyx_pybuffernd_xyz_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-30T17:31:21,844 | ^ 2024-05-30T17:31:21,849 mdtraj/formats/xtc/xtc.c:8058:23: warning: ‘__pyx_pybuffernd_xyz_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,849 8058 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_xyz_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T17:31:21,849 | ^ 2024-05-30T17:31:21,853 mdtraj/formats/xtc/xtc.c:8018:23: warning: ‘__pyx_pybuffernd_time_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,854 8018 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_time_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T17:31:21,854 | ^ 2024-05-30T17:31:21,858 mdtraj/formats/xtc/xtc.c:8000:23: warning: ‘__pyx_pybuffernd_step_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,858 8000 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_step_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T17:31:21,859 | ^ 2024-05-30T17:31:21,862 mdtraj/formats/xtc/xtc.c:8076:23: warning: ‘__pyx_pybuffernd_prec_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,863 8076 | } else if (unlikely(__pyx_t_40 >= __pyx_pybuffernd_prec_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T17:31:21,863 | ^ 2024-05-30T17:31:21,867 mdtraj/formats/xtc/xtc.c:8038:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,867 8038 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_box_stride.diminfo[2].shape)) __pyx_t_6 = 2; 2024-05-30T17:31:21,867 | ^ 2024-05-30T17:31:21,872 mdtraj/formats/xtc/xtc.c:8034:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,872 8034 | } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_box_stride.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-30T17:31:21,872 | ^ 2024-05-30T17:31:21,877 mdtraj/formats/xtc/xtc.c:8030:23: warning: ‘__pyx_pybuffernd_box_stride.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,877 8030 | } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_box_stride.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T17:31:21,877 | ^ 2024-05-30T17:31:21,881 mdtraj/formats/xtc/xtc.c:7653:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,881 7653 | } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_framebuffer.diminfo[1].shape)) __pyx_t_6 = 1; 2024-05-30T17:31:21,882 | ^ 2024-05-30T17:31:21,886 mdtraj/formats/xtc/xtc.c:7649:17: warning: ‘__pyx_pybuffernd_framebuffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:21,886 7649 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_framebuffer.diminfo[0].shape)) __pyx_t_6 = 0; 2024-05-30T17:31:21,886 | ^ 2024-05-30T17:31:26,450 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/xtc.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:31:26,633 building 'mdtraj.formats.trr' extension 2024-05-30T17:31:26,634 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 -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdr_seek.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:26,750 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:26,882 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2024-05-30T17:31:26,882 mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:26,883 788 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-30T17:31:26,883 | ^~~~~~ 2024-05-30T17:31:26,883 mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:26,883 785 | int smallidx, minidx, maxidx; 2024-05-30T17:31:26,883 | ^~~~~~ 2024-05-30T17:31:26,890 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2024-05-30T17:31:26,890 mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:26,890 1016 | int errval=1; 2024-05-30T17:31:26,890 | ^~~~~~ 2024-05-30T17:31:26,894 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’: 2024-05-30T17:31:26,895 mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:26,895 1305 | int smallnum, smaller, larger, i, is_smaller, run; 2024-05-30T17:31:26,895 | ^~~~~~ 2024-05-30T17:31:26,896 mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:26,896 1302 | int smallidx, minidx, maxidx; 2024-05-30T17:31:26,896 | ^~~~~~ 2024-05-30T17:31:26,904 mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2024-05-30T17:31:26,905 mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable] 2024-05-30T17:31:26,905 1509 | int errval=1; 2024-05-30T17:31:26,905 | ^~~~~~ 2024-05-30T17:31:29,013 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 -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:29,661 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 -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/trr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:29,981 In file included from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-30T17:31:29,981 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T17:31:29,981 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-30T17:31:29,981 from mdtraj/formats/xtc/trr.c:781: 2024-05-30T17:31:29,981 /tmp/pip-build-env-3nq7ycgc/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] 2024-05-30T17:31:29,982 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T17:31:29,982 | ^~~~~~~ 2024-05-30T17:31:36,781 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_18_write’: 2024-05-30T17:31:36,781 mdtraj/formats/xtc/trr.c:693:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:36,781 693 | #define PyInt_FromLong PyLong_FromLong 2024-05-30T17:31:36,781 | ^~~~~~~~~~~~~~~ 2024-05-30T17:31:36,787 mdtraj/formats/xtc/trr.c:11073:7: note: ‘__pyx_v_status’ was declared here 2024-05-30T17:31:36,788 11073 | int __pyx_v_status; 2024-05-30T17:31:36,788 | ^~~~~~~~~~~~~~ 2024-05-30T17:31:46,540 mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_read’: 2024-05-30T17:31:46,545 mdtraj/formats/xtc/trr.c:8426:19: warning: ‘__pyx_pybuffernd_forces.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,545 8426 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_forces.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-30T17:31:46,546 | ^ 2024-05-30T17:31:46,550 mdtraj/formats/xtc/trr.c:8422:19: warning: ‘__pyx_pybuffernd_forces.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,551 8422 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_forces.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T17:31:46,551 | ^ 2024-05-30T17:31:46,551 mdtraj/formats/xtc/trr.c:1929:95: warning: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,551 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-30T17:31:46,552 | ^ 2024-05-30T17:31:46,555 mdtraj/formats/xtc/trr.c:6963:21: note: ‘__pyx_pybuffernd_forces.diminfo[0].strides’ was declared here 2024-05-30T17:31:46,555 6963 | __Pyx_LocalBuf_ND __pyx_pybuffernd_forces; 2024-05-30T17:31:46,555 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:31:46,560 mdtraj/formats/xtc/trr.c:8416:59: warning: ‘__pyx_pybuffernd_forces.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,560 8416 | __pyx_t_29 += __pyx_pybuffernd_forces.diminfo[0].shape; 2024-05-30T17:31:46,560 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-30T17:31:46,565 mdtraj/formats/xtc/trr.c:8369:19: warning: ‘__pyx_pybuffernd_vel.diminfo[2].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,565 8369 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_vel.diminfo[2].shape)) __pyx_t_5 = 2; 2024-05-30T17:31:46,565 | ^ 2024-05-30T17:31:46,570 mdtraj/formats/xtc/trr.c:8365:19: warning: ‘__pyx_pybuffernd_vel.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,570 8365 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_vel.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T17:31:46,570 | ^ 2024-05-30T17:31:46,570 mdtraj/formats/xtc/trr.c:1929:95: warning: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,571 1929 | #define __Pyx_BufPtrCContig3d(type, buf, i0, s0, i1, s1, i2, s2) ((type)((char*)buf + i0 * s0 + i1 * s1) + i2) 2024-05-30T17:31:46,571 | ^ 2024-05-30T17:31:46,574 mdtraj/formats/xtc/trr.c:6979:21: note: ‘__pyx_pybuffernd_vel.diminfo[0].strides’ was declared here 2024-05-30T17:31:46,574 6979 | __Pyx_LocalBuf_ND __pyx_pybuffernd_vel; 2024-05-30T17:31:46,575 | ^~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:31:46,579 mdtraj/formats/xtc/trr.c:8359:56: warning: ‘__pyx_pybuffernd_vel.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,579 8359 | __pyx_t_29 += __pyx_pybuffernd_vel.diminfo[0].shape; 2024-05-30T17:31:46,579 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2024-05-30T17:31:46,583 mdtraj/formats/xtc/trr.c:8759:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,583 8759 | } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_xyz_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T17:31:46,583 | ^ 2024-05-30T17:31:46,588 mdtraj/formats/xtc/trr.c:8755:17: warning: ‘__pyx_pybuffernd_xyz_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,589 8755 | } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_xyz_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-30T17:31:46,589 | ^ 2024-05-30T17:31:46,593 mdtraj/formats/xtc/trr.c:8600:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,594 8600 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_vel_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T17:31:46,594 | ^ 2024-05-30T17:31:46,599 mdtraj/formats/xtc/trr.c:8596:19: warning: ‘__pyx_pybuffernd_vel_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,599 8596 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_vel_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-30T17:31:46,599 | ^ 2024-05-30T17:31:46,603 mdtraj/formats/xtc/trr.c:8652:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[1].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,603 8652 | } else if (unlikely(__pyx_t_37 >= __pyx_pybuffernd_forces_buffer.diminfo[1].shape)) __pyx_t_5 = 1; 2024-05-30T17:31:46,603 | ^ 2024-05-30T17:31:46,608 mdtraj/formats/xtc/trr.c:8648:19: warning: ‘__pyx_pybuffernd_forces_buffer.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:31:46,609 8648 | } else if (unlikely(__pyx_t_36 >= __pyx_pybuffernd_forces_buffer.diminfo[0].shape)) __pyx_t_5 = 0; 2024-05-30T17:31:46,609 | ^ 2024-05-30T17:31:53,041 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdr_seek.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/xtc/trr.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:31:53,213 building 'mdtraj.formats.dcd' extension 2024-05-30T17:31:53,214 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd 2024-05-30T17:31:53,215 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src 2024-05-30T17:31:53,215 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/dcd.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:31:53,533 In file included from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-30T17:31:53,533 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T17:31:53,533 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-30T17:31:53,534 from mdtraj/formats/dcd/dcd.c:779: 2024-05-30T17:31:53,534 /tmp/pip-build-env-3nq7ycgc/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] 2024-05-30T17:31:53,534 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T17:31:53,534 | ^~~~~~~ 2024-05-30T17:32:00,786 mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’: 2024-05-30T17:32:00,786 mdtraj/formats/dcd/dcd.c:691:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:32:00,786 691 | #define PyInt_FromLong PyLong_FromLong 2024-05-30T17:32:00,786 | ^~~~~~~~~~~~~~~ 2024-05-30T17:32:00,789 mdtraj/formats/dcd/dcd.c:5442:7: note: ‘__pyx_v_i’ was declared here 2024-05-30T17:32:00,789 5442 | int __pyx_v_i; 2024-05-30T17:32:00,789 | ^~~~~~~~~ 2024-05-30T17:32:03,896 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 -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src/dcdplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:32:05,221 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:32:05,357 building 'mdtraj.formats.dtr' extension 2024-05-30T17:32:05,358 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr 2024-05-30T17:32:05,359 creating build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src 2024-05-30T17:32:05,360 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 -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/dtr.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:32:05,606 In file included from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-30T17:32:05,607 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T17:32:05,607 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-30T17:32:05,607 from mdtraj/formats/dtr/dtr.cpp:800: 2024-05-30T17:32:05,607 /tmp/pip-build-env-3nq7ycgc/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] 2024-05-30T17:32:05,607 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T17:32:05,607 | ^~~~~~~ 2024-05-30T17:32:17,784 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 -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src/dtrplugin.o -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:32:19,443 mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’: 2024-05-30T17:32:19,443 mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-30T17:32:19,443 486 | fprintf(stderr, "non-constant framesize at frame %ld\n", i); 2024-05-30T17:32:19,443 | ~~^ ~ 2024-05-30T17:32:19,443 | | | 2024-05-30T17:32:19,443 | | size_t {aka unsigned int} 2024-05-30T17:32:19,444 | long int 2024-05-30T17:32:19,444 | %d 2024-05-30T17:32:19,444 mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-30T17:32:19,444 487 | printf("size %d framesize %d\n\n", 2024-05-30T17:32:19,444 | ~^ 2024-05-30T17:32:19,444 | | 2024-05-30T17:32:19,445 | int 2024-05-30T17:32:19,445 | %lld 2024-05-30T17:32:19,445 488 | keys[i].size(), m_framesize); 2024-05-30T17:32:19,445 | ~~~~~~~~~~~~~~ 2024-05-30T17:32:19,445 | | 2024-05-30T17:32:19,445 | uint64_t {aka long long unsigned int} 2024-05-30T17:32:19,445 mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-30T17:32:19,446 487 | printf("size %d framesize %d\n\n", 2024-05-30T17:32:19,446 | ~^ 2024-05-30T17:32:19,446 | | 2024-05-30T17:32:19,446 | int 2024-05-30T17:32:19,446 | %lld 2024-05-30T17:32:19,446 488 | keys[i].size(), m_framesize); 2024-05-30T17:32:19,447 | ~~~~~~~~~~~ 2024-05-30T17:32:19,447 | | 2024-05-30T17:32:19,447 | uint64_t {aka long long unsigned int} 2024-05-30T17:32:19,447 mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-30T17:32:19,447 494 | "non-constant time interval at frame %ld\n", i); 2024-05-30T17:32:19,447 | ~~^ ~ 2024-05-30T17:32:19,447 | | | 2024-05-30T17:32:19,448 | | size_t {aka unsigned int} 2024-05-30T17:32:19,448 | long int 2024-05-30T17:32:19,448 | %d 2024-05-30T17:32:19,448 mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-05-30T17:32:19,448 499 | fprintf(stderr, "unexpected offset for frame %ld\n", i); 2024-05-30T17:32:19,448 | ~~^ ~ 2024-05-30T17:32:19,448 | | | 2024-05-30T17:32:19,449 | | size_t {aka unsigned int} 2024-05-30T17:32:19,449 | long int 2024-05-30T17:32:19,449 | %d 2024-05-30T17:32:19,572 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-30T17:32:19,572 mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-30T17:32:19,573 1301 | fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n", 2024-05-30T17:32:19,573 | ~~^ 2024-05-30T17:32:19,573 | | 2024-05-30T17:32:19,573 | long int 2024-05-30T17:32:19,573 | %lld 2024-05-30T17:32:19,573 1302 | 3*natoms, pos.count); 2024-05-30T17:32:19,573 | ~~~~~~~~~ 2024-05-30T17:32:19,574 | | 2024-05-30T17:32:19,574 | uint64_t {aka long long unsigned int} 2024-05-30T17:32:19,574 mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-30T17:32:19,574 1310 | fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n", 2024-05-30T17:32:19,574 | ~~^ 2024-05-30T17:32:19,574 | | 2024-05-30T17:32:19,575 | long int 2024-05-30T17:32:19,575 | %lld 2024-05-30T17:32:19,575 1311 | 3*natoms, vel.count); 2024-05-30T17:32:19,575 | ~~~~~~~~~ 2024-05-30T17:32:19,575 | | 2024-05-30T17:32:19,575 | uint64_t {aka long long unsigned int} 2024-05-30T17:32:19,598 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’: 2024-05-30T17:32:19,598 mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2024-05-30T17:32:19,598 1572 | fprintf(stderr, "VELOCITY field has %ld values; expected %d\n", 2024-05-30T17:32:19,598 | ~~^ 2024-05-30T17:32:19,598 | | 2024-05-30T17:32:19,598 | long int 2024-05-30T17:32:19,599 | %lld 2024-05-30T17:32:19,599 1573 | velblob.count, 3*natoms); 2024-05-30T17:32:19,599 | ~~~~~~~~~~~~~ 2024-05-30T17:32:19,599 | | 2024-05-30T17:32:19,599 | uint64_t {aka long long unsigned int} 2024-05-30T17:32:20,626 mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’: 2024-05-30T17:32:20,626 mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized] 2024-05-30T17:32:20,626 680 | : std::runtime_error(text + strerror(eno)), eno(_eno){} 2024-05-30T17:32:20,627 | ~~~~~~~~^~~~~ 2024-05-30T17:32:22,856 In file included from /usr/include/c++/10/map:60, 2024-05-30T17:32:22,857 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-30T17:32:22,857 /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-30T17:32:22,857 /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T17:32:22,857 2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-30T17:32:22,857 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:22,919 /usr/include/c++/10/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-30T17:32:22,920 /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T17:32:22,920 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2024-05-30T17:32:22,920 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:22,920 /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T17:32:22,977 In file included from /usr/include/c++/10/map:61, 2024-05-30T17:32:22,978 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-30T17:32:22,978 /usr/include/c++/10/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]’: 2024-05-30T17:32:22,978 /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T17:32:22,978 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-30T17:32:22,978 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:22,978 521 | std::forward_as_tuple(std::move(__k)), 2024-05-30T17:32:22,978 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:22,978 522 | std::tuple<>()); 2024-05-30T17:32:22,979 | ~~~~~~~~~~~~~~~ 2024-05-30T17:32:23,751 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’: 2024-05-30T17:32:23,752 mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2024-05-30T17:32:23,752 706 | sprintf(sub, "%03x/", i); 2024-05-30T17:32:23,752 | ^~~~ 2024-05-30T17:32:23,752 mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646] 2024-05-30T17:32:23,752 706 | sprintf(sub, "%03x/", i); 2024-05-30T17:32:23,752 | ^~~~~~~ 2024-05-30T17:32:23,752 mdtraj/formats/dtr/src/dtrplugin.cxx:706:9: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 6 2024-05-30T17:32:23,753 706 | sprintf(sub, "%03x/", i); 2024-05-30T17:32:23,753 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2024-05-30T17:32:23,753 mdtraj/formats/dtr/src/dtrplugin.cxx:714:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 2024-05-30T17:32:23,753 714 | sprintf(subsub, "%03x", j); 2024-05-30T17:32:23,753 | ^~~~ 2024-05-30T17:32:23,753 mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646] 2024-05-30T17:32:23,753 714 | sprintf(subsub, "%03x", j); 2024-05-30T17:32:23,754 | ^~~~~~ 2024-05-30T17:32:23,754 mdtraj/formats/dtr/src/dtrplugin.cxx:714:13: note: ‘sprintf’ output between 4 and 9 bytes into a destination of size 6 2024-05-30T17:32:23,754 714 | sprintf(subsub, "%03x", j); 2024-05-30T17:32:23,754 | ~~~~~~~^~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:24,166 mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’: 2024-05-30T17:32:24,167 mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-30T17:32:24,167 667 | sprintf(answer, "%03x/", d1); 2024-05-30T17:32:24,167 | ^ 2024-05-30T17:32:24,167 mdtraj/formats/dtr/src/dtrplugin.cxx:667:13: note: ‘sprintf’ output between 5 and 10 bytes into a destination of size 9 2024-05-30T17:32:24,167 667 | sprintf(answer, "%03x/", d1); 2024-05-30T17:32:24,167 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:24,168 mdtraj/formats/dtr/src/dtrplugin.cxx:665:28: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] 2024-05-30T17:32:24,168 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-30T17:32:24,168 | ^~~~ 2024-05-30T17:32:24,168 mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646] 2024-05-30T17:32:24,168 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-30T17:32:24,168 | ^~~~~~~~~~~~ 2024-05-30T17:32:24,168 mdtraj/formats/dtr/src/dtrplugin.cxx:665:13: note: ‘sprintf’ output between 9 and 19 bytes into a destination of size 9 2024-05-30T17:32:24,169 665 | sprintf(answer, "%03x/%03x/", d1, d2); 2024-05-30T17:32:24,169 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:26,888 In file included from /usr/include/c++/10/map:61, 2024-05-30T17:32:26,888 from mdtraj/formats/dtr/src/dtrplugin.cxx:53: 2024-05-30T17:32:26,889 /usr/include/c++/10/bits/stl_map.h: In member function ‘int desres::molfile::DtrReader::frame_from_bytes(const void*, uint64_t, molfile_timestep_t*) const’: 2024-05-30T17:32:26,889 /usr/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1 2024-05-30T17:32:26,889 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2024-05-30T17:32:26,889 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:26,889 521 | std::forward_as_tuple(std::move(__k)), 2024-05-30T17:32:26,889 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-30T17:32:26,890 522 | std::tuple<>()); 2024-05-30T17:32:26,890 | ~~~~~~~~~~~~~~~ 2024-05-30T17:32:32,022 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-cpython-39/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:32:32,404 building 'mdtraj._rmsd' extension 2024-05-30T17:32:32,405 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd 2024-05-30T17:32:32,406 creating build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src 2024-05-30T17:32:32,407 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 -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:06,780 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 -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:06,986 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 -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:07,232 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 -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:07,896 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_rmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:33:08,251 building 'mdtraj._lprmsd' extension 2024-05-30T17:33:08,253 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_lprmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_lprmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:08,526 In file included from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-30T17:33:08,526 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T17:33:08,526 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-30T17:33:08,526 from mdtraj/rmsd/_lprmsd.cpp:809: 2024-05-30T17:33:08,527 /tmp/pip-build-env-3nq7ycgc/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] 2024-05-30T17:33:08,527 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T17:33:08,527 | ^~~~~~~ 2024-05-30T17:33:19,217 mdtraj/rmsd/_lprmsd.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7_lprmsd_lprmsd(PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*, PyLongObject*, PyLongObject*)’: 2024-05-30T17:33:19,217 mdtraj/rmsd/_lprmsd.cpp:4099:14: warning: ‘__pyx_pybuffernd_ref_xyz_frame_dis.__Pyx_LocalBuf_ND::diminfo[0].__Pyx_Buf_DimInfo::shape’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:33:19,218 4099 | } else if (unlikely(__pyx_t_34 >= __pyx_pybuffernd_ref_xyz_frame_dis.diminfo[0].shape)) __pyx_t_33 = 0; 2024-05-30T17:33:19,218 | ^~ 2024-05-30T17:33:29,766 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/Munkres.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/Munkres.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:32,156 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:32,355 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/euclidean_permutation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/euclidean_permutation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:33,389 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/fancy_index.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/fancy_index.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:33,679 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/rotation.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:33,936 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 -Imdtraj/rmsd -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:34,625 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/_lprmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/Munkres.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/euclidean_permutation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/fancy_index.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/rotation.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:33:34,952 building 'mdtraj.core.lib.libtheobald' extension 2024-05-30T17:33:34,953 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 -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/theobald_rmsd.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o -O3 -funroll-loops --std=c++11 2024-05-30T17:33:35,613 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 -Imdtraj/rmsd/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/src/center.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o -O3 -funroll-loops --std=c++11 2024-05-30T17:33:35,809 arm-linux-gnueabihf-gcc-ar rcs build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/theobald_rmsd.o build/temp.linux-armv7l-cpython-39/mdtraj/rmsd/src/center.o 2024-05-30T17:33:35,846 building 'mdtraj.geometry._geometry' extension 2024-05-30T17:33:35,847 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry 2024-05-30T17:33:35,847 creating build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src 2024-05-30T17:33:35,849 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 -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/_geometry.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/_geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:33:36,105 In file included from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822, 2024-05-30T17:33:36,106 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-30T17:33:36,106 from /tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2024-05-30T17:33:36,106 from mdtraj/geometry/src/_geometry.cpp:811: 2024-05-30T17:33:36,106 /tmp/pip-build-env-3nq7ycgc/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] 2024-05-30T17:33:36,106 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-30T17:33:36,106 | ^~~~~~~ 2024-05-30T17:34:05,463 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 -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dssp.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dssp.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:34:21,830 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 -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/geometry.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/geometry.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:34:25,335 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 -Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/sasa.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/sasa.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:34:26,315 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/_geometry.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dssp.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/geometry.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/sasa.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:34:26,767 building 'mdtraj.geometry.drid' extension 2024-05-30T17:34:26,768 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 -Imdtraj/geometry/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/drid.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/drid.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:34:51,164 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 -Imdtraj/geometry/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/dridkernels.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dridkernels.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:34:51,743 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 -Imdtraj/geometry/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/moments.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/moments.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:34:51,860 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/drid.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/dridkernels.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/moments.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:34:52,191 building 'mdtraj.geometry.neighbors' extension 2024-05-30T17:34:52,192 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 -Imdtraj/geometry/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighbors.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:35:15,120 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 -Imdtraj/geometry/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighbors.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighbors.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:35:16,256 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighbors.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:35:16,593 building 'mdtraj.geometry.neighborlist' extension 2024-05-30T17:35:16,595 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 -Imdtraj/geometry/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/neighborlist.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:35:36,950 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 -Imdtraj/geometry/include -I/tmp/pip-build-env-3nq7ycgc/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/geometry/src/neighborlist.cpp -o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighborlist.o -fopenmp -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare 2024-05-30T17:35:41,224 mdtraj/geometry/src/neighborlist.cpp: In function ‘std::vector > _compute_neighborlist(const float*, int, float, const float*)’: 2024-05-30T17:35:41,224 mdtraj/geometry/src/neighborlist.cpp:50:53: warning: ‘periodicBoxVectors[0][0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:35:41,224 50 | periodicBoxSize[0] = periodicBoxVectors[0][0]; 2024-05-30T17:35:41,224 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-30T17:35:41,225 mdtraj/geometry/src/neighborlist.cpp:51:53: warning: ‘periodicBoxVectors[1][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:35:41,225 51 | periodicBoxSize[1] = periodicBoxVectors[1][1]; 2024-05-30T17:35:41,225 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-30T17:35:41,225 mdtraj/geometry/src/neighborlist.cpp:52:53: warning: ‘periodicBoxVectors[2][2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:35:41,225 52 | periodicBoxSize[2] = periodicBoxVectors[2][2]; 2024-05-30T17:35:41,225 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-30T17:35:41,226 mdtraj/geometry/src/neighborlist.cpp:56:45: warning: ‘periodicBoxVectors[0][1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-05-30T17:35:41,226 56 | triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 || 2024-05-30T17:35:41,226 | ~~~~~~~~~~~~~~~~~~~~~~~^ 2024-05-30T17:35:42,222 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.o build/temp.linux-armv7l-cpython-39/mdtraj/geometry/src/neighborlist.o -L/usr/lib -lgomp -o build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so 2024-05-30T17:35:42,590 installing to build/bdist.linux-armv7l/wheel 2024-05-30T17:35:42,591 running install 2024-05-30T17:35:42,617 running install_lib 2024-05-30T17:35:42,626 creating build/bdist.linux-armv7l 2024-05-30T17:35:42,627 creating build/bdist.linux-armv7l/wheel 2024-05-30T17:35:42,629 creating build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T17:35:42,630 creating build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-30T17:35:42,632 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/shift_wrappers.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-30T17:35:42,634 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-30T17:35:42,636 copying build/lib.linux-armv7l-cpython-39/mdtraj/nmr/scalar_couplings.py -> build/bdist.linux-armv7l/wheel/mdtraj/nmr 2024-05-30T17:35:42,639 creating build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,640 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/psf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,643 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/registry.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,645 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,658 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,660 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lh5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,662 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdbx.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,665 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hdf5.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,668 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gro.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,671 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/lammpstrj.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,674 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,709 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,732 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mdcrd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,735 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/prmtop.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,737 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/amberrst.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,740 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,762 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/arc.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,765 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/netcdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,768 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/xyzfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,771 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/hoomdxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,773 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/mol2.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,776 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-30T17:35:42,777 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbfile.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-30T17:35:42,780 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/pdbstructure.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-30T17:35:42,783 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb 2024-05-30T17:35:42,785 creating build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-30T17:35:42,787 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/residues.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-30T17:35:42,790 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/pdb/data/pdbNames.xml -> build/bdist.linux-armv7l/wheel/mdtraj/formats/pdb/data 2024-05-30T17:35:42,792 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/gsd.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,794 copying build/lib.linux-armv7l-cpython-39/mdtraj/formats/openmmxml.py -> build/bdist.linux-armv7l/wheel/mdtraj/formats 2024-05-30T17:35:42,796 copying build/lib.linux-armv7l-cpython-39/mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T17:35:42,819 copying build/lib.linux-armv7l-cpython-39/mdtraj/io.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T17:35:42,822 creating build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,823 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/internal.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,826 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,853 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/angle.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,855 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,857 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/thermodynamic_properties.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,859 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,885 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dihedral.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,888 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,911 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/shape.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,913 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/alignment.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,915 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/distance.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,918 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/sasa.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,920 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rg.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,922 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/rdf.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,925 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/hbond.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,927 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,980 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/dssp.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,982 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/order.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,984 copying build/lib.linux-armv7l-cpython-39/mdtraj/geometry/contact.py -> build/bdist.linux-armv7l/wheel/mdtraj/geometry 2024-05-30T17:35:42,987 copying build/lib.linux-armv7l-cpython-39/mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T17:35:43,016 creating build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T17:35:43,017 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T17:35:43,019 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docstrings.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T17:35:43,021 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/docscrape.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T17:35:43,023 copying build/lib.linux-armv7l-cpython-39/mdtraj/testing/testing.py -> build/bdist.linux-armv7l/wheel/mdtraj/testing 2024-05-30T17:35:43,025 copying build/lib.linux-armv7l-cpython-39/mdtraj/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T17:35:43,028 creating build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-30T17:35:43,028 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdinspect.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-30T17:35:43,031 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-30T17:35:43,032 copying build/lib.linux-armv7l-cpython-39/mdtraj/scripts/mdconvert.py -> build/bdist.linux-armv7l/wheel/mdtraj/scripts 2024-05-30T17:35:43,035 creating build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T17:35:43,036 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/selection.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T17:35:43,039 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/residue_names.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T17:35:43,041 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T17:35:43,042 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/trajectory.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T17:35:43,047 creating build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-30T17:35:43,048 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/center.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-30T17:35:43,050 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/theobald_rmsd.h -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-30T17:35:43,052 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/lib/libtheobald.a -> build/bdist.linux-armv7l/wheel/mdtraj/core/lib 2024-05-30T17:35:43,055 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/topology.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T17:35:43,059 copying build/lib.linux-armv7l-cpython-39/mdtraj/core/element.py -> build/bdist.linux-armv7l/wheel/mdtraj/core 2024-05-30T17:35:43,061 copying build/lib.linux-armv7l-cpython-39/mdtraj/version.py -> build/bdist.linux-armv7l/wheel/mdtraj 2024-05-30T17:35:43,064 creating build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T17:35:43,064 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/xtcreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T17:35:43,067 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/netcdfreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T17:35:43,068 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T17:35:43,070 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/dcdreporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T17:35:43,072 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/basereporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T17:35:43,074 copying build/lib.linux-armv7l-cpython-39/mdtraj/reporters/hdf5reporter.py -> build/bdist.linux-armv7l/wheel/mdtraj/reporters 2024-05-30T17:35:43,077 creating build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,078 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/rotation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,080 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/zipped.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,082 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/contextmanagers.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,084 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,085 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/validation.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,088 creating build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,089 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/basedimension.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,091 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/constants.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,093 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/standard_dimensions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,095 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,098 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/__init__.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,100 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/mymatrix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,102 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/quantity.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,105 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/baseunit.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,108 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_definitions.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,110 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/prefix.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,112 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/doctests.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,115 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_operators.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,117 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unit/unit_math.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils/unit 2024-05-30T17:35:43,119 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/unitcell.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,121 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/delay_import.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,123 copying build/lib.linux-armv7l-cpython-39/mdtraj/utils/singleton.py -> build/bdist.linux-armv7l/wheel/mdtraj/utils 2024-05-30T17:35:43,125 running install_egg_info 2024-05-30T17:35:43,138 running egg_info 2024-05-30T17:35:43,144 writing mdtraj.egg-info/PKG-INFO 2024-05-30T17:35:43,147 writing dependency_links to mdtraj.egg-info/dependency_links.txt 2024-05-30T17:35:43,149 writing entry points to mdtraj.egg-info/entry_points.txt 2024-05-30T17:35:43,150 writing requirements to mdtraj.egg-info/requires.txt 2024-05-30T17:35:43,151 writing top-level names to mdtraj.egg-info/top_level.txt 2024-05-30T17:35:43,185 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,185 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,186 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,186 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,186 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,186 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,186 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,186 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,187 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,187 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,188 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,188 dependency /tmp/pip-build-env-3nq7ycgc/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 2024-05-30T17:35:43,203 reading manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-30T17:35:43,220 reading manifest template 'MANIFEST.in' 2024-05-30T17:35:43,793 no previously-included directories found matching '__pycache__' 2024-05-30T17:35:43,794 no previously-included directories found matching '*.pyc' 2024-05-30T17:35:43,794 adding license file 'LICENSE' 2024-05-30T17:35:43,810 writing manifest file 'mdtraj.egg-info/SOURCES.txt' 2024-05-30T17:35:43,812 Copying mdtraj.egg-info to build/bdist.linux-armv7l/wheel/mdtraj-1.10.0-py3.9.egg-info 2024-05-30T17:35:43,825 running install_scripts 2024-05-30T17:35:43,880 creating build/bdist.linux-armv7l/wheel/mdtraj-1.10.0.dist-info/WHEEL 2024-05-30T17:35:43,882 creating '/tmp/pip-wheel-m55eg420/.tmp-vk2lyxl8/mdtraj-1.10.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-30T17:35:43,885 adding 'mdtraj/__init__.py' 2024-05-30T17:35:44,125 adding 'mdtraj/_lprmsd.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:44,496 adding 'mdtraj/_rmsd.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:44,510 adding 'mdtraj/io.py' 2024-05-30T17:35:44,511 adding 'mdtraj/version.py' 2024-05-30T17:35:44,513 adding 'mdtraj/core/__init__.py' 2024-05-30T17:35:44,516 adding 'mdtraj/core/element.py' 2024-05-30T17:35:44,519 adding 'mdtraj/core/residue_names.py' 2024-05-30T17:35:44,521 adding 'mdtraj/core/selection.py' 2024-05-30T17:35:44,529 adding 'mdtraj/core/topology.py' 2024-05-30T17:35:44,538 adding 'mdtraj/core/trajectory.py' 2024-05-30T17:35:44,540 adding 'mdtraj/core/lib/center.h' 2024-05-30T17:35:44,550 adding 'mdtraj/core/lib/libtheobald.a' 2024-05-30T17:35:44,552 adding 'mdtraj/core/lib/theobald_rmsd.h' 2024-05-30T17:35:44,554 adding 'mdtraj/formats/__init__.py' 2024-05-30T17:35:44,558 adding 'mdtraj/formats/amberrst.py' 2024-05-30T17:35:44,560 adding 'mdtraj/formats/arc.py' 2024-05-30T17:35:44,718 adding 'mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:45,137 adding 'mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:45,154 adding 'mdtraj/formats/gro.py' 2024-05-30T17:35:45,156 adding 'mdtraj/formats/gsd.py' 2024-05-30T17:35:45,160 adding 'mdtraj/formats/hdf5.py' 2024-05-30T17:35:45,162 adding 'mdtraj/formats/hoomdxml.py' 2024-05-30T17:35:45,165 adding 'mdtraj/formats/lammpstrj.py' 2024-05-30T17:35:45,168 adding 'mdtraj/formats/lh5.py' 2024-05-30T17:35:45,171 adding 'mdtraj/formats/mdcrd.py' 2024-05-30T17:35:45,173 adding 'mdtraj/formats/mol2.py' 2024-05-30T17:35:45,176 adding 'mdtraj/formats/netcdf.py' 2024-05-30T17:35:45,177 adding 'mdtraj/formats/openmmxml.py' 2024-05-30T17:35:45,180 adding 'mdtraj/formats/pdbx.py' 2024-05-30T17:35:45,181 adding 'mdtraj/formats/prmtop.py' 2024-05-30T17:35:45,183 adding 'mdtraj/formats/psf.py' 2024-05-30T17:35:45,185 adding 'mdtraj/formats/registry.py' 2024-05-30T17:35:45,452 adding 'mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:45,718 adding 'mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:45,728 adding 'mdtraj/formats/xyzfile.py' 2024-05-30T17:35:45,730 adding 'mdtraj/formats/pdb/__init__.py' 2024-05-30T17:35:45,734 adding 'mdtraj/formats/pdb/pdbfile.py' 2024-05-30T17:35:45,739 adding 'mdtraj/formats/pdb/pdbstructure.py' 2024-05-30T17:35:45,741 adding 'mdtraj/formats/pdb/data/pdbNames.xml' 2024-05-30T17:35:45,743 adding 'mdtraj/formats/pdb/data/residues.xml' 2024-05-30T17:35:45,745 adding 'mdtraj/geometry/__init__.py' 2024-05-30T17:35:46,271 adding 'mdtraj/geometry/_geometry.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:46,291 adding 'mdtraj/geometry/alignment.py' 2024-05-30T17:35:46,293 adding 'mdtraj/geometry/angle.py' 2024-05-30T17:35:46,295 adding 'mdtraj/geometry/contact.py' 2024-05-30T17:35:46,298 adding 'mdtraj/geometry/dihedral.py' 2024-05-30T17:35:46,300 adding 'mdtraj/geometry/distance.py' 2024-05-30T17:35:46,578 adding 'mdtraj/geometry/drid.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:46,588 adding 'mdtraj/geometry/dssp.py' 2024-05-30T17:35:46,591 adding 'mdtraj/geometry/hbond.py' 2024-05-30T17:35:46,594 adding 'mdtraj/geometry/internal.py' 2024-05-30T17:35:46,893 adding 'mdtraj/geometry/neighborlist.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:47,177 adding 'mdtraj/geometry/neighbors.cpython-39-arm-linux-gnueabihf.so' 2024-05-30T17:35:47,188 adding 'mdtraj/geometry/order.py' 2024-05-30T17:35:47,190 adding 'mdtraj/geometry/rdf.py' 2024-05-30T17:35:47,191 adding 'mdtraj/geometry/rg.py' 2024-05-30T17:35:47,193 adding 'mdtraj/geometry/sasa.py' 2024-05-30T17:35:47,195 adding 'mdtraj/geometry/shape.py' 2024-05-30T17:35:47,196 adding 'mdtraj/geometry/thermodynamic_properties.py' 2024-05-30T17:35:47,198 adding 'mdtraj/nmr/__init__.py' 2024-05-30T17:35:47,199 adding 'mdtraj/nmr/scalar_couplings.py' 2024-05-30T17:35:47,201 adding 'mdtraj/nmr/shift_wrappers.py' 2024-05-30T17:35:47,203 adding 'mdtraj/reporters/__init__.py' 2024-05-30T17:35:47,205 adding 'mdtraj/reporters/basereporter.py' 2024-05-30T17:35:47,206 adding 'mdtraj/reporters/dcdreporter.py' 2024-05-30T17:35:47,208 adding 'mdtraj/reporters/hdf5reporter.py' 2024-05-30T17:35:47,209 adding 'mdtraj/reporters/netcdfreporter.py' 2024-05-30T17:35:47,211 adding 'mdtraj/reporters/xtcreporter.py' 2024-05-30T17:35:47,212 adding 'mdtraj/scripts/__init__.py' 2024-05-30T17:35:47,215 adding 'mdtraj/scripts/mdconvert.py' 2024-05-30T17:35:47,217 adding 'mdtraj/scripts/mdinspect.py' 2024-05-30T17:35:47,219 adding 'mdtraj/testing/__init__.py' 2024-05-30T17:35:47,221 adding 'mdtraj/testing/docscrape.py' 2024-05-30T17:35:47,223 adding 'mdtraj/testing/docstrings.py' 2024-05-30T17:35:47,225 adding 'mdtraj/testing/testing.py' 2024-05-30T17:35:47,227 adding 'mdtraj/utils/__init__.py' 2024-05-30T17:35:47,228 adding 'mdtraj/utils/contextmanagers.py' 2024-05-30T17:35:47,230 adding 'mdtraj/utils/delay_import.py' 2024-05-30T17:35:47,231 adding 'mdtraj/utils/rotation.py' 2024-05-30T17:35:47,233 adding 'mdtraj/utils/singleton.py' 2024-05-30T17:35:47,234 adding 'mdtraj/utils/unitcell.py' 2024-05-30T17:35:47,236 adding 'mdtraj/utils/validation.py' 2024-05-30T17:35:47,238 adding 'mdtraj/utils/zipped.py' 2024-05-30T17:35:47,240 adding 'mdtraj/utils/unit/__init__.py' 2024-05-30T17:35:47,242 adding 'mdtraj/utils/unit/basedimension.py' 2024-05-30T17:35:47,243 adding 'mdtraj/utils/unit/baseunit.py' 2024-05-30T17:35:47,245 adding 'mdtraj/utils/unit/constants.py' 2024-05-30T17:35:47,248 adding 'mdtraj/utils/unit/doctests.py' 2024-05-30T17:35:47,250 adding 'mdtraj/utils/unit/mymatrix.py' 2024-05-30T17:35:47,252 adding 'mdtraj/utils/unit/prefix.py' 2024-05-30T17:35:47,257 adding 'mdtraj/utils/unit/quantity.py' 2024-05-30T17:35:47,258 adding 'mdtraj/utils/unit/standard_dimensions.py' 2024-05-30T17:35:47,262 adding 'mdtraj/utils/unit/unit.py' 2024-05-30T17:35:47,264 adding 'mdtraj/utils/unit/unit_definitions.py' 2024-05-30T17:35:47,266 adding 'mdtraj/utils/unit/unit_math.py' 2024-05-30T17:35:47,267 adding 'mdtraj/utils/unit/unit_operators.py' 2024-05-30T17:35:47,273 adding 'mdtraj-1.10.0.dist-info/LICENSE' 2024-05-30T17:35:47,274 adding 'mdtraj-1.10.0.dist-info/METADATA' 2024-05-30T17:35:47,275 adding 'mdtraj-1.10.0.dist-info/WHEEL' 2024-05-30T17:35:47,276 adding 'mdtraj-1.10.0.dist-info/entry_points.txt' 2024-05-30T17:35:47,277 adding 'mdtraj-1.10.0.dist-info/top_level.txt' 2024-05-30T17:35:47,279 adding 'mdtraj-1.10.0.dist-info/RECORD' 2024-05-30T17:35:47,347 removing build/bdist.linux-armv7l/wheel 2024-05-30T17:35:48,110 Building wheel for mdtraj (pyproject.toml): finished with status 'done' 2024-05-30T17:35:48,238 Created wheel for mdtraj: filename=mdtraj-1.10.0-cp39-cp39-linux_armv7l.whl size=6059958 sha256=68704957676ac0a3c67be88f4f5d81b88229b356d3c65b872b92469e5b9b8de1 2024-05-30T17:35:48,239 Stored in directory: /tmp/pip-ephem-wheel-cache-krm7yxf7/wheels/4f/17/89/f855cce8e6394e9029e1b972cb623c8813b706d3d1ca81832f 2024-05-30T17:35:48,256 Successfully built mdtraj 2024-05-30T17:35:48,403 Removed build tracker: '/tmp/pip-build-tracker-n4ag0wfq'