2025-09-08T00:46:31,285 Created temporary directory: /tmp/pip-build-tracker-6i72_usq 2025-09-08T00:46:31,285 Initialized build tracking at /tmp/pip-build-tracker-6i72_usq 2025-09-08T00:46:31,286 Created build tracker: /tmp/pip-build-tracker-6i72_usq 2025-09-08T00:46:31,286 Entered build tracker: /tmp/pip-build-tracker-6i72_usq 2025-09-08T00:46:31,286 Created temporary directory: /tmp/pip-wheel-tzknklh8 2025-09-08T00:46:31,290 Created temporary directory: /tmp/pip-ephem-wheel-cache-s4cu_yeu 2025-09-08T00:46:31,352 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T00:46:31,355 2 location(s) to search for versions of mdtraj: 2025-09-08T00:46:31,355 * https://pypi.org/simple/mdtraj/ 2025-09-08T00:46:31,355 * https://www.piwheels.org/simple/mdtraj/ 2025-09-08T00:46:31,355 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/ 2025-09-08T00:46:31,356 Getting page https://pypi.org/simple/mdtraj/ 2025-09-08T00:46:31,357 Found index url https://pypi.org/simple/ 2025-09-08T00:46:31,434 Fetched page https://pypi.org/simple/mdtraj/ as application/vnd.pypi.simple.v1+json 2025-09-08T00:46:31,452 Found link https://files.pythonhosted.org/packages/cb/82/93ced2a2e5d37f36330fe3e74081fdd4ce8f933ebd16b4fab14cb5c6c29c/mdtraj-0.3.tar.gz (from https://pypi.org/simple/mdtraj/), version: 0.3 2025-09-08T00:46:31,453 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 2025-09-08T00:46:31,453 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/) 2025-09-08T00:46:31,453 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 2025-09-08T00:46:31,454 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 2025-09-08T00:46:31,454 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 2025-09-08T00:46:31,454 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/) 2025-09-08T00:46:31,454 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/) 2025-09-08T00:46:31,455 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/) 2025-09-08T00:46:31,455 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/) 2025-09-08T00:46:31,455 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 2025-09-08T00:46:31,455 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 2025-09-08T00:46:31,455 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/) 2025-09-08T00:46:31,456 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/) 2025-09-08T00:46:31,456 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/) 2025-09-08T00:46:31,456 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 2025-09-08T00:46:31,456 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 2025-09-08T00:46:31,457 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 2025-09-08T00:46:31,457 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 2025-09-08T00:46:31,457 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 2025-09-08T00:46:31,458 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 2025-09-08T00:46:31,458 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 2025-09-08T00:46:31,458 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 2025-09-08T00:46:31,458 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 2025-09-08T00:46:31,459 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 2025-09-08T00:46:31,459 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 2025-09-08T00:46:31,459 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 2025-09-08T00:46:31,460 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/) 2025-09-08T00:46:31,460 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 2025-09-08T00:46:31,460 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 2025-09-08T00:46:31,460 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 2025-09-08T00:46:31,461 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 2025-09-08T00:46:31,461 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 2025-09-08T00:46:31,461 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/) 2025-09-08T00:46:31,461 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/) 2025-09-08T00:46:31,462 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/) 2025-09-08T00:46:31,462 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 2025-09-08T00:46:31,462 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 2025-09-08T00:46:31,462 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 2025-09-08T00:46:31,463 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 2025-09-08T00:46:31,463 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 2025-09-08T00:46:31,463 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 2025-09-08T00:46:31,464 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 2025-09-08T00:46:31,464 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 2025-09-08T00:46:31,464 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 2025-09-08T00:46:31,464 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 2025-09-08T00:46:31,465 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 2025-09-08T00:46:31,465 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 2025-09-08T00:46:31,465 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/) 2025-09-08T00:46:31,465 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/) 2025-09-08T00:46:31,466 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/) 2025-09-08T00:46:31,466 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 2025-09-08T00:46:31,466 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 2025-09-08T00:46:31,466 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 2025-09-08T00:46:31,467 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 2025-09-08T00:46:31,467 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 2025-09-08T00:46:31,467 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 2025-09-08T00:46:31,468 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 2025-09-08T00:46:31,468 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 2025-09-08T00:46:31,468 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 2025-09-08T00:46:31,468 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 2025-09-08T00:46:31,469 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 2025-09-08T00:46:31,469 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 2025-09-08T00:46:31,469 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 2025-09-08T00:46:31,470 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 2025-09-08T00:46:31,470 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/) 2025-09-08T00:46:31,470 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/) 2025-09-08T00:46:31,470 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/) 2025-09-08T00:46:31,470 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/) 2025-09-08T00:46:31,471 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 2025-09-08T00:46:31,471 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/) 2025-09-08T00:46:31,471 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/) 2025-09-08T00:46:31,471 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/) 2025-09-08T00:46:31,471 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/) 2025-09-08T00:46:31,472 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 2025-09-08T00:46:31,472 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 2025-09-08T00:46:31,472 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/) 2025-09-08T00:46:31,472 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 2025-09-08T00:46:31,473 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/) 2025-09-08T00:46:31,473 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 2025-09-08T00:46:31,473 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 2025-09-08T00:46:31,473 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 2025-09-08T00:46:31,474 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/cd/3a/379ed1598326f81b58780695671311ee0e67604881af98b8d1ecc3ac3ec2/mdtraj-1.10.0-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,474 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/61/59/065625dbdb7d7b30469793fb8a066d359dce25a3aef147429d53486686cd/mdtraj-1.10.0-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,474 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/f9/04/bbcffdebc024702b2b17b19b3119f013b44230cfc68a9f61079a6e25c879/mdtraj-1.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,474 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/f5/70/45c94c7d42d0fa42df392b0e72e861ef14ec6a62dc7aef602ddee57120c3/mdtraj-1.10.0-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,474 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/a2/4d/1754c96a113ba6ce4e2cb6e2e1e2552b20436ddea3ea23d7adafa1cd57d6/mdtraj-1.10.0-cp311-cp311-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,475 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/b9/90/6360c9b1ae390950aa354e57760a3770fa798b4dd4d1c2559d457f3dd25f/mdtraj-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,475 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/a3/71/e23a45d315d19fcddb11f2fe4e31213533126f723bf411ac9af4b97df458/mdtraj-1.10.0-cp312-cp312-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,475 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/d4/e6/4335566e7d2a28a1e1e0f2bf37d207dafdc001c1407375146a2810ce8a12/mdtraj-1.10.0-cp312-cp312-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,475 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/b5/68/a0769942f6c4fa30ef382b0cb03ef9a74f19c47c777adb60ba236d4ffa9d/mdtraj-1.10.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) 2025-09-08T00:46:31,475 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 2025-09-08T00:46:31,476 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/d7/aa/a72c8ee54482d07e56592699ead14f6ec30c821719e9034160d654f30ac7/mdtraj-1.10.1-cp310-cp310-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,476 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/53/5d/561a3147f4df30b4cbb1ed9cc457dc750a4a2f118c3f4bc936ea84c89435/mdtraj-1.10.1-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,476 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/3e/c5/fc7bdab48b103288d10c59490281bf8d3a5f501b5ac719bcac13a0c0e98f/mdtraj-1.10.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,476 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/a8/93/dd1a61fb77efef1600b3bcbca66be63595d02f96f97488345f483f3d569a/mdtraj-1.10.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,476 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/ea/a3/7db7ec5f38e51280bf0389fb218f7142b80f6eb11a7c22f23f41916b200d/mdtraj-1.10.1-cp311-cp311-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,476 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/3f/75/7906fa05665021f2b81132120befca644be7b66a0475d5230d4783293da9/mdtraj-1.10.1-cp311-cp311-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,477 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/0b/16/87a1a02a9b6c83f2aef786f3e67ea7cd26e0312b0938a64fa7396d76223a/mdtraj-1.10.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,477 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/0a/34/d480e05b0986b8f3b9eafa087c182bb2d8dc19697a02e4e2f57676eabf3b/mdtraj-1.10.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,477 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/e1/a3/382f893064f1cac9ed3f92bb83df1e42a52236577040526b02abff07e502/mdtraj-1.10.1-cp312-cp312-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,477 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/2d/43/cc504cf953b23fc7b95800a4544511358618d54641499a8fcbc99c48984e/mdtraj-1.10.1-cp312-cp312-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,477 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/4a/32/23bb14a54d3b285cf45fb19880f337814f50a248db633aead1941ea1ed77/mdtraj-1.10.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,477 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/ab/6f/7a655c74d548ecdd567dbe26458207e85bcec0ed93374d7f3a5622602004/mdtraj-1.10.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,478 Found link https://files.pythonhosted.org/packages/d1/dd/347f10de449ef8d50400d4312bfe2e2dc4f2d1a8ca7ff60693ed30bc44aa/mdtraj-1.10.1.tar.gz (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9), version: 1.10.1 2025-09-08T00:46:31,478 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/18/94/492d50b7c68a44eac7dc42cfe189ffd1156d68ff0ea0e447d55b8ee3fa16/mdtraj-1.10.2-cp310-cp310-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,479 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/3c/95/4083e43a353a946415d5a111a7d0096ed43570791da16e2d859bb65aa48c/mdtraj-1.10.2-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,479 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/88/07/0118a054abacd22a8d7ee1c87a2fee8333be9560f3c9518dcbb547fce0fc/mdtraj-1.10.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,479 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/d6/fd/3e059c411340cd5f76468d0fd28175a86e1fcf298e4d32bce6bb553dcfe1/mdtraj-1.10.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,479 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/7d/65/ff06cbdd9723e4ac80188b79aefd475b6b754d7faefe1c0aec97da57529c/mdtraj-1.10.2-cp311-cp311-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,479 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/a6/35/103fa38566119782dbb190ddc81765d07fb015691d14b84371b87a5d381c/mdtraj-1.10.2-cp311-cp311-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,479 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/83/7b/8087de2cc8cf9ba6259d7a5b5cd94c5e8981ce0f65e15ec1cc10a2ec876e/mdtraj-1.10.2-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,480 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/17/44/dcdfa851b913c7d307dc9688e74e943c842f6e0fae31484e233af51c49d3/mdtraj-1.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,480 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/27/1a/73bba93744c648a587cf808387037049c8ce97766efc3b54ae28f1c6a934/mdtraj-1.10.2-cp312-cp312-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,480 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/34/6e/841699cb16aca879e5b67e19370cb5916fcfb8d022ee63d8afb5b3261c41/mdtraj-1.10.2-cp312-cp312-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,480 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/42/b0/526511ed4d9360d14411d20a9793435fbf92f45ff75ca2135edd56f1a24a/mdtraj-1.10.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,480 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/bb/da/c2a0bc6808d350a3fd59fa70c0b4300b04b2045ed5e2edef93cc114ab8b3/mdtraj-1.10.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,481 Found link https://files.pythonhosted.org/packages/78/23/a3614328c93d8d431007d4585eea77eeb16b00910c9a6a98d3e82e893162/mdtraj-1.10.2.tar.gz (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9), version: 1.10.2 2025-09-08T00:46:31,481 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/31/7d/b4e1bb04658ebc4bf29c8d5cc4a98d5a2701e43f0ae65cc3e622f607f9f1/mdtraj-1.10.3-cp310-cp310-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,481 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/db/6f/9193143fbc62b5b65eb14e19bd9180e5d711c7816f8ff5abeb6c17802e2c/mdtraj-1.10.3-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,481 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/0d/4c/1b38f92711176aa3f99133a8b746f8a0a1f94bb9d2ba8d5ff8911fd35162/mdtraj-1.10.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,481 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/01/00/3847180c37f85e93f8a9d0347d547743a2d0b5718bdf61e9159723ae4324/mdtraj-1.10.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,481 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/62/20/01cd9e58a17c674afb0f3326703c5cbe60647e542107282bae79b98ffb5b/mdtraj-1.10.3-cp311-cp311-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,482 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/15/bb/1d0633ec89ff7dcc62f445b086c238f9b42a34d09dcd039bf29fdbe49af5/mdtraj-1.10.3-cp311-cp311-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,482 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/04/81/a0a18977681e07daf962a2e0fe46c9caf356734f00bcf0efbb2622c20460/mdtraj-1.10.3-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,482 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/50/45/fc9f5e5b4caa6f3b08aaf6c84a79d4888922ec81a09b80bb19fbe723618e/mdtraj-1.10.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,482 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/09/d1/674b0afc09cde4ad48fe7f130435a65a80f6d4be9ba4ebb3453440350c97/mdtraj-1.10.3-cp312-cp312-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,482 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/56/ba/f5893ee34e8da5e739cd442c0aab3d954edc2cedd741f4319bf12d3c9e63/mdtraj-1.10.3-cp312-cp312-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,483 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/66/c5/7afbe5ee8f398679ee9207b01b1bbd2507da881dd6758ad7e09279bb5e51/mdtraj-1.10.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,483 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/30/6b/424ac2a6845367d4fe86f05a8ba8b29d9872a810cfe634c4372d2cee4bd9/mdtraj-1.10.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,483 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/ac/a7/c1a282f186baf11405258cf07dbc16500211fe73e77e6fa53fecc4730aa0/mdtraj-1.10.3-cp313-cp313-macosx_10_13_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,483 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/8b/74/d0a60f2d0aec79136d2a25d5c8f0f774e74e188e3667d3d4485a21023434/mdtraj-1.10.3-cp313-cp313-macosx_11_0_arm64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,483 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/76/e1/fe0e305b5adee67b6c1a5d0b3a29739233856347af2b5fa86f54f22914f2/mdtraj-1.10.3-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,483 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/26/b7/cd45c6bae1566572d96bda6e749c63886c9c6ded079e34615376de5fe26e/mdtraj-1.10.3-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,484 Found link https://files.pythonhosted.org/packages/6a/ef/44c34823d2cfd935b76be102ea41bce3a2e688c3d84ccff9029df0c1ff96/mdtraj-1.10.3.tar.gz (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.9), version: 1.10.3 2025-09-08T00:46:31,484 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/f8/bc/1a6d273467a24dad5048bf527288a7bbe997ecee8342f6e8fdd7465c9132/mdtraj-1.11.0-cp311-cp311-macosx_10_9_universal2.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,484 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/09/dc/37bd8a22c66d05a293979d8d8cf1de5e6c03d21ebd6950b6a839c8d8a16b/mdtraj-1.11.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,484 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/4c/48/6fc195907c056df9b6ff6442bb39c5dd433b971b9deaecf6d18a0761efa8/mdtraj-1.11.0-cp311-cp311-win_amd64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,484 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/21/71/56adb24577052f2cd6f9b678da908e8e2d7963db3a88faff39792be43903/mdtraj-1.11.0-cp312-cp312-macosx_10_13_universal2.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,485 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/50/af/7d65be36619befb29b51b6118a97121de6685720af7f4cfd6ff1902ca7eb/mdtraj-1.11.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,485 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/d2/8f/fd05aa3613fad29b3a779e3384797d2b64aa329bcfd18d25f8fb9c0d725e/mdtraj-1.11.0-cp312-cp312-win_amd64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,485 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/9c/8f/adbeabf14f27a2befd021548c5d8e696ca129924e0473863fb0e9e546f27/mdtraj-1.11.0-cp313-cp313-macosx_10_13_universal2.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,485 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/b5/c4/4a2e8db0f24c1deb85f4719d54a0a52c56403e17db61ddd72a95d39e07d6/mdtraj-1.11.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,485 Skipping link: No binaries permitted for mdtraj: https://files.pythonhosted.org/packages/ac/17/239ae1869fa0f6fe11e42388f5d1e094ac774f4d122767722f0451523989/mdtraj-1.11.0-cp313-cp313-win_amd64.whl (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11) 2025-09-08T00:46:31,486 Found link https://files.pythonhosted.org/packages/49/87/04f21b321e7bb6f3e09b5339df51699b8caae4846796175845bbc44f298b/mdtraj-1.11.0.tar.gz (from https://pypi.org/simple/mdtraj/) (requires-python:>=3.11), version: 1.11.0 2025-09-08T00:46:31,486 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdtraj/ 2025-09-08T00:46:31,487 Getting page https://www.piwheels.org/simple/mdtraj/ 2025-09-08T00:46:31,488 Found index url https://www.piwheels.org/simple/ 2025-09-08T00:46:31,581 Fetched page https://www.piwheels.org/simple/mdtraj/ as text/html 2025-09-08T00:46:31,589 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.3-cp311-cp311-linux_armv6l.whl#sha256=75f9a9246dfd7dc4377f0d185394b5f34042e27b8ab386432aa17f33c1d89cec (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,589 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.3-cp311-cp311-linux_armv7l.whl#sha256=75f9a9246dfd7dc4377f0d185394b5f34042e27b8ab386432aa17f33c1d89cec (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,589 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.3-cp39-cp39-linux_armv6l.whl#sha256=81ead85c4a08ebb7c9e54f9234d3f3a2ede24410abc9a145652fc3da235d615a (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,590 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.3-cp39-cp39-linux_armv7l.whl#sha256=81ead85c4a08ebb7c9e54f9234d3f3a2ede24410abc9a145652fc3da235d615a (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,590 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.2-cp311-cp311-linux_armv6l.whl#sha256=724ebc6fd5cda59276a1154289427dfbd8d8b68659d945dd0ac555bac4538138 (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,590 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.2-cp311-cp311-linux_armv7l.whl#sha256=724ebc6fd5cda59276a1154289427dfbd8d8b68659d945dd0ac555bac4538138 (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,590 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.2-cp39-cp39-linux_armv6l.whl#sha256=5bb8dc2b195b92a55c431970bb2e4fdbcd94df1455986a4e4bac932d90a5aaef (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,590 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.2-cp39-cp39-linux_armv7l.whl#sha256=5bb8dc2b195b92a55c431970bb2e4fdbcd94df1455986a4e4bac932d90a5aaef (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,590 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.1-cp311-cp311-linux_armv6l.whl#sha256=31a939c91c9ccc0d7aa9c68f13811069407c1289789667063e395b6467663bb6 (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,591 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.1-cp311-cp311-linux_armv7l.whl#sha256=31a939c91c9ccc0d7aa9c68f13811069407c1289789667063e395b6467663bb6 (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,591 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.1-cp39-cp39-linux_armv6l.whl#sha256=48fb95fa6bab2afa810800a5471e7da438638b5139562e3d6af826aa77f56ce2 (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,591 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.1-cp39-cp39-linux_armv7l.whl#sha256=48fb95fa6bab2afa810800a5471e7da438638b5139562e3d6af826aa77f56ce2 (from https://www.piwheels.org/simple/mdtraj/) (requires-python:>=3.9) 2025-09-08T00:46:31,591 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp311-cp311-linux_armv6l.whl#sha256=b303bd85a6fe8b1a38c95c47fe66624944c9783bcccb08afdc041d048d4a489b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,591 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp311-cp311-linux_armv7l.whl#sha256=b303bd85a6fe8b1a38c95c47fe66624944c9783bcccb08afdc041d048d4a489b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,591 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp37-cp37m-linux_armv6l.whl#sha256=1f004eae3fa9fdf88cbe94eb85a14d097452e4c35a5e57a695cd836a33e38fd5 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,591 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp37-cp37m-linux_armv7l.whl#sha256=1f004eae3fa9fdf88cbe94eb85a14d097452e4c35a5e57a695cd836a33e38fd5 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,592 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp39-cp39-linux_armv6l.whl#sha256=68704957676ac0a3c67be88f4f5d81b88229b356d3c65b872b92469e5b9b8de1 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,592 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0-cp39-cp39-linux_armv7l.whl#sha256=68704957676ac0a3c67be88f4f5d81b88229b356d3c65b872b92469e5b9b8de1 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,592 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp311-cp311-linux_armv6l.whl#sha256=bb4a20fe32bcfb564d4efcd3c10b2d6c88728eecacf8bd1b53dd402e387c444f (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,592 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp311-cp311-linux_armv7l.whl#sha256=bb4a20fe32bcfb564d4efcd3c10b2d6c88728eecacf8bd1b53dd402e387c444f (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,592 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp37-cp37m-linux_armv6l.whl#sha256=cb090c5366b7b76d938daa16ca5a431a4fe751344ec320479b3ba8134a6ff4bd (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,592 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp37-cp37m-linux_armv7l.whl#sha256=cb090c5366b7b76d938daa16ca5a431a4fe751344ec320479b3ba8134a6ff4bd (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,593 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv6l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,593 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc2-cp39-cp39-linux_armv7l.whl#sha256=4b7226f511a99286314bd00f0ce2a1b66fb3458713efc1c18b24a423d3a9125b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,593 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp37-cp37m-linux_armv6l.whl#sha256=355ab9108c6d079032d3b97eaa3ad76e261893dcd45a07b62c5e8a493600e06d (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,593 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp37-cp37m-linux_armv7l.whl#sha256=355ab9108c6d079032d3b97eaa3ad76e261893dcd45a07b62c5e8a493600e06d (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,593 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv6l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,593 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp311-cp311-linux_armv7l.whl#sha256=1f13d3792f9062c44ac99e3a61bac7128f1d77d93ad42f3f9c61dfddc485a84b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,594 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv6l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,594 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.10.0rc1-cp39-cp39-linux_armv7l.whl#sha256=961ec4359feef74c9b79bbcb1a2d5d0d2f59cb2683684d2c1e0b7b4e3f5c5ce7 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,594 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv6l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,594 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp37-cp37m-linux_armv7l.whl#sha256=45caac608640d5fdbd5a0dc7be3baa8a1c53ed2e1fcbca505c369265d39e81e5 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,594 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv6l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,594 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp39-cp39-linux_armv7l.whl#sha256=17beda35d5d81436d38431065a7f636ee87acf201220a1b7cadb44bdfef8e1ac (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,594 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv6l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,595 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.9-cp311-cp311-linux_armv7l.whl#sha256=f34a54dd8a65075466e688fb90472889487b918f53dd300a13cb4a843ede142b (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,595 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv6l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,595 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp37-cp37m-linux_armv7l.whl#sha256=5a6ef10c614114b37ec371fa3404f7d834f894d9576f3e3a4940d1587074f8e1 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,595 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv6l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,595 Skipping link: No binaries permitted for mdtraj: https://archive1.piwheels.org/simple/mdtraj/mdtraj-1.9.8-cp39-cp39-linux_armv7l.whl#sha256=985dc85d46bda039eaa12656d7b3a95c340a2a298e8b580c0af8b9b7dca435c3 (from https://www.piwheels.org/simple/mdtraj/) 2025-09-08T00:46:31,596 Skipping link: not a file: https://www.piwheels.org/simple/mdtraj/ 2025-09-08T00:46:31,596 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2025-09-08T00:46:31,627 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates 2025-09-08T00:46:31,628 Collecting mdtraj==1.2.0 2025-09-08T00:46:31,630 Created temporary directory: /tmp/pip-unpack-j7jxinvq 2025-09-08T00:46:31,798 Downloading mdtraj-1.2.0.zip (6.7 MB) 2025-09-08T00:46:33,276 Added mdtraj==1.2.0 from https://files.pythonhosted.org/packages/ad/60/131151a1dacdf1fb8aa2afb20d2f7865802ee8a654f5c46bf0990cd44b77/mdtraj-1.2.0.zip to build tracker '/tmp/pip-build-tracker-6i72_usq' 2025-09-08T00:46:33,278 Running setup.py (path:/tmp/pip-wheel-tzknklh8/mdtraj_b63165ccb7e44ef6ba1d0d71db467c96/setup.py) egg_info for package mdtraj 2025-09-08T00:46:33,278 Created temporary directory: /tmp/pip-pip-egg-info-5dip8rwv 2025-09-08T00:46:33,278 Preparing metadata (setup.py): started 2025-09-08T00:46:33,279 Running command python setup.py egg_info 2025-09-08T00:46:34,326 Using built-in specs. 2025-09-08T00:46:34,326 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T00:46:34,327 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T00:46:34,327 Target: arm-linux-gnueabihf 2025-09-08T00:46:34,327 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --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-libstdcxx-backtrace --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+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T00:46:34,327 Thread model: posix 2025-09-08T00:46:34,327 Supported LTO compression algorithms: zlib zstd 2025-09-08T00:46:34,327 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T00:46:53,895 performance hint: MDTraj/rmsd/_rmsd.pyx:171:62: Use boundscheck(False) for faster access 2025-09-08T00:46:53,896 performance hint: MDTraj/rmsd/_rmsd.pyx:171:87: Use boundscheck(False) for faster access 2025-09-08T00:46:53,896 performance hint: MDTraj/rmsd/_rmsd.pyx:171:103: Use boundscheck(False) for faster access 2025-09-08T00:46:53,897 performance hint: MDTraj/rmsd/_rmsd.pyx:172:21: Use boundscheck(False) for faster access 2025-09-08T00:46:54,027 C compiler: 2025-09-08T00:46:54,027 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T00:46:54,027 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T00:46:54,027 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T00:46:54,028 Compiling MDTraj/formats/xtc/xtc.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/formats/xtc/trr.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/formats/dcd/dcd.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/formats/binpos/binpos.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/formats/dtr/dtr.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/rmsd/_rmsd.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/rmsd/_lprmsd.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/geometry/src/_geometry.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/geometry/drid.pyx because it changed. 2025-09-08T00:46:54,028 Compiling MDTraj/geometry/neighbors.pyx because it changed. 2025-09-08T00:46:54,029 [ 1/10] Cythonizing MDTraj/formats/binpos/binpos.pyx 2025-09-08T00:46:54,029 [ 2/10] Cythonizing MDTraj/formats/dcd/dcd.pyx 2025-09-08T00:46:54,029 [ 3/10] Cythonizing MDTraj/formats/dtr/dtr.pyx 2025-09-08T00:46:54,029 [ 4/10] Cythonizing MDTraj/formats/xtc/trr.pyx 2025-09-08T00:46:54,029 [ 5/10] Cythonizing MDTraj/formats/xtc/xtc.pyx 2025-09-08T00:46:54,029 [ 6/10] Cythonizing MDTraj/geometry/drid.pyx 2025-09-08T00:46:54,029 [ 7/10] Cythonizing MDTraj/geometry/neighbors.pyx 2025-09-08T00:46:54,029 [ 8/10] Cythonizing MDTraj/geometry/src/_geometry.pyx 2025-09-08T00:46:54,029 [ 9/10] Cythonizing MDTraj/rmsd/_lprmsd.pyx 2025-09-08T00:46:54,029 [10/10] Cythonizing MDTraj/rmsd/_rmsd.pyx 2025-09-08T00:46:54,471 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T00:46:54,471 !! 2025-09-08T00:46:54,471 ******************************************************************************** 2025-09-08T00:46:54,471 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T00:46:54,472 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T00:46:54,472 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T00:46:54,472 ******************************************************************************** 2025-09-08T00:46:54,472 !! 2025-09-08T00:46:54,472 self._finalize_license_expression() 2025-09-08T00:46:54,558 running egg_info 2025-09-08T00:46:54,647 creating /tmp/pip-pip-egg-info-5dip8rwv/mdtraj.egg-info 2025-09-08T00:46:54,648 writing /tmp/pip-pip-egg-info-5dip8rwv/mdtraj.egg-info/PKG-INFO 2025-09-08T00:46:54,649 writing dependency_links to /tmp/pip-pip-egg-info-5dip8rwv/mdtraj.egg-info/dependency_links.txt 2025-09-08T00:46:54,650 writing entry points to /tmp/pip-pip-egg-info-5dip8rwv/mdtraj.egg-info/entry_points.txt 2025-09-08T00:46:54,650 writing top-level names to /tmp/pip-pip-egg-info-5dip8rwv/mdtraj.egg-info/top_level.txt 2025-09-08T00:46:54,651 writing manifest file '/tmp/pip-pip-egg-info-5dip8rwv/mdtraj.egg-info/SOURCES.txt' 2025-09-08T00:46:54,965 reading manifest file '/tmp/pip-pip-egg-info-5dip8rwv/mdtraj.egg-info/SOURCES.txt' 2025-09-08T00:46:54,966 reading manifest template 'MANIFEST.in' 2025-09-08T00:46:54,993 writing manifest file '/tmp/pip-pip-egg-info-5dip8rwv/mdtraj.egg-info/SOURCES.txt' 2025-09-08T00:46:56,495 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T00:46:56,500 Source in /tmp/pip-wheel-tzknklh8/mdtraj_b63165ccb7e44ef6ba1d0d71db467c96 has version 1.2.0, which satisfies requirement mdtraj==1.2.0 from https://files.pythonhosted.org/packages/ad/60/131151a1dacdf1fb8aa2afb20d2f7865802ee8a654f5c46bf0990cd44b77/mdtraj-1.2.0.zip 2025-09-08T00:46:56,500 Removed mdtraj==1.2.0 from https://files.pythonhosted.org/packages/ad/60/131151a1dacdf1fb8aa2afb20d2f7865802ee8a654f5c46bf0990cd44b77/mdtraj-1.2.0.zip from build tracker '/tmp/pip-build-tracker-6i72_usq' 2025-09-08T00:46:56,503 Created temporary directory: /tmp/pip-unpack-k07u_4ob 2025-09-08T00:46:56,504 Created temporary directory: /tmp/pip-unpack-1bk4l34z 2025-09-08T00:46:56,504 Building wheels for collected packages: mdtraj 2025-09-08T00:46:56,505 Created temporary directory: /tmp/pip-wheel-1lk86_zm 2025-09-08T00:46:56,506 DEPRECATION: Building 'mdtraj' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'mdtraj'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T00:46:56,507 Building wheel for mdtraj (setup.py): started 2025-09-08T00:46:56,508 Destination directory: /tmp/pip-wheel-1lk86_zm 2025-09-08T00:46:56,508 Running command python setup.py bdist_wheel 2025-09-08T00:46:57,491 C compiler: 2025-09-08T00:46:57,496 Using built-in specs. 2025-09-08T00:46:57,497 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T00:46:57,498 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T00:46:57,498 Target: arm-linux-gnueabihf 2025-09-08T00:46:57,499 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --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-libstdcxx-backtrace --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+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T00:46:57,499 Thread model: posix 2025-09-08T00:46:57,499 Supported LTO compression algorithms: zlib zstd 2025-09-08T00:46:57,499 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T00:46:58,986 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T00:46:59,667 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T00:47:00,394 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T00:47:01,693 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T00:47:01,693 !! 2025-09-08T00:47:01,694 ******************************************************************************** 2025-09-08T00:47:01,694 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T00:47:01,694 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T00:47:01,694 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T00:47:01,694 ******************************************************************************** 2025-09-08T00:47:01,694 !! 2025-09-08T00:47:01,695 self._finalize_license_expression() 2025-09-08T00:47:01,695 running bdist_wheel 2025-09-08T00:47:02,049 running build 2025-09-08T00:47:02,049 running build_py 2025-09-08T00:47:02,141 creating build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T00:47:02,141 copying scripts/mdinspect.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T00:47:02,142 copying scripts/mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T00:47:02,143 copying scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/scripts 2025-09-08T00:47:02,144 copying MDTraj/version.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T00:47:02,145 copying MDTraj/io.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T00:47:02,145 copying MDTraj/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj 2025-09-08T00:47:02,146 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,147 copying MDTraj/utils/validation.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,147 copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,148 copying MDTraj/utils/test.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,149 copying MDTraj/utils/six.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,150 copying MDTraj/utils/rotation.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,150 copying MDTraj/utils/ffi.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,151 copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,151 copying MDTraj/utils/contextmanagers.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,152 copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils 2025-09-08T00:47:02,153 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,154 copying MDTraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,154 copying MDTraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,155 copying MDTraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,156 copying MDTraj/utils/unit/unit.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,157 copying MDTraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,157 copying MDTraj/utils/unit/quantity.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,158 copying MDTraj/utils/unit/prefix.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,159 copying MDTraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,159 copying MDTraj/utils/unit/doctests.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,160 copying MDTraj/utils/unit/constants.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,161 copying MDTraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,162 copying MDTraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,162 copying MDTraj/utils/unit/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/unit 2025-09-08T00:47:02,163 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T00:47:02,163 copying MDTraj/utils/external/pyparsing.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T00:47:02,165 copying MDTraj/utils/external/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external 2025-09-08T00:47:02,166 creating build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T00:47:02,166 copying MDTraj/utils/external/astor/treewalk.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T00:47:02,167 copying MDTraj/utils/external/astor/misc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T00:47:02,167 copying MDTraj/utils/external/astor/codegen.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T00:47:02,168 copying MDTraj/utils/external/astor/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/utils/external/astor 2025-09-08T00:47:02,170 creating build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,170 copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,171 copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,171 copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,172 copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,173 copying MDTraj/tests/test_topology.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,173 copying MDTraj/tests/test_selection.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,174 copying MDTraj/tests/test_rmsd_memmap.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,175 copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,175 copying MDTraj/tests/test_restart.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,176 copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,177 copying MDTraj/tests/test_quaternion.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,177 copying MDTraj/tests/test_psf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,178 copying MDTraj/tests/test_prmtop.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,179 copying MDTraj/tests/test_nmr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,179 copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,180 copying MDTraj/tests/test_mol2.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,181 copying MDTraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,181 copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,182 copying MDTraj/tests/test_lprmsd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,183 copying MDTraj/tests/test_lh5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,183 copying MDTraj/tests/test_lammpstrj.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,184 copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,185 copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,185 copying MDTraj/tests/test_gro.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,186 copying MDTraj/tests/test_element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,187 copying MDTraj/tests/test_dtr.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,187 copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,188 copying MDTraj/tests/test_crd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,189 copying MDTraj/tests/test_capi.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,189 copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,190 copying MDTraj/tests/test_arc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,191 copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/tests 2025-09-08T00:47:02,191 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T00:47:02,192 copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T00:47:02,193 copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T00:47:02,193 copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T00:47:02,194 copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T00:47:02,195 copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/testing 2025-09-08T00:47:02,196 creating build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T00:47:02,196 copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T00:47:02,197 copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T00:47:02,197 copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T00:47:02,198 copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T00:47:02,199 copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/reporters 2025-09-08T00:47:02,200 creating build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T00:47:02,200 copying MDTraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T00:47:02,201 copying MDTraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T00:47:02,201 copying MDTraj/nmr/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/nmr 2025-09-08T00:47:02,202 creating build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T00:47:02,203 copying MDTraj/html/trajectory_widget.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T00:47:02,203 copying MDTraj/html/linked_heatmap.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T00:47:02,204 copying MDTraj/html/install.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T00:47:02,205 copying MDTraj/html/imagebutton_widget.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T00:47:02,205 copying MDTraj/html/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/html 2025-09-08T00:47:02,206 creating build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,207 copying MDTraj/geometry/sasa.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,207 copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,208 copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,209 copying MDTraj/geometry/hbond.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,209 copying MDTraj/geometry/dssp.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,210 copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,211 copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,212 copying MDTraj/geometry/contact.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,212 copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,213 copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,214 copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry 2025-09-08T00:47:02,215 creating build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,215 copying MDTraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,216 copying MDTraj/geometry/tests/test_neighbors.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,216 copying MDTraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,217 copying MDTraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,218 copying MDTraj/geometry/tests/test_dssp.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,218 copying MDTraj/geometry/tests/test_drid.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,219 copying MDTraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,220 copying MDTraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,220 copying MDTraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,221 copying MDTraj/geometry/tests/test_angles.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,222 copying MDTraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,223 copying MDTraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/geometry/tests 2025-09-08T00:47:02,224 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,224 copying MDTraj/formats/registry.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,225 copying MDTraj/formats/psf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,225 copying MDTraj/formats/prmtop.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,226 copying MDTraj/formats/openmmxml.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,227 copying MDTraj/formats/netcdf.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,227 copying MDTraj/formats/mol2.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,228 copying MDTraj/formats/mdcrd.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,229 copying MDTraj/formats/lh5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,230 copying MDTraj/formats/lammpstrj.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,230 copying MDTraj/formats/hdf5.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,231 copying MDTraj/formats/gro.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,232 copying MDTraj/formats/arc.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,233 copying MDTraj/formats/amberrst.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,234 copying MDTraj/formats/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats 2025-09-08T00:47:02,234 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T00:47:02,235 copying MDTraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T00:47:02,236 copying MDTraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T00:47:02,236 copying MDTraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb 2025-09-08T00:47:02,237 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T00:47:02,238 copying MDTraj/formats/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T00:47:02,238 copying MDTraj/formats/pdb/tests/test_element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T00:47:02,239 copying MDTraj/formats/pdb/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/tests 2025-09-08T00:47:02,240 creating build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T00:47:02,240 copying MDTraj/core/trajectory.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T00:47:02,241 copying MDTraj/core/topology.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T00:47:02,242 copying MDTraj/core/selection.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T00:47:02,243 copying MDTraj/core/residue_names.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T00:47:02,244 copying MDTraj/core/element.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T00:47:02,244 copying MDTraj/core/__init__.py -> build/lib.linux-armv7l-cpython-313/mdtraj/core 2025-09-08T00:47:02,258 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,258 copying MDTraj/testing/reference/tz2.truncoct.parm7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,263 copying MDTraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,264 copying MDTraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,265 copying MDTraj/testing/reference/README.md -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,265 copying MDTraj/testing/reference/overflow.crd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,272 copying MDTraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,272 copying MDTraj/testing/reference/nitrogen.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,276 copying MDTraj/testing/reference/nitrogen.arc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,280 copying MDTraj/testing/reference/ncinpcrd.rst7 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,281 copying MDTraj/testing/reference/native2.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,282 copying MDTraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,282 copying MDTraj/testing/reference/native.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,283 copying MDTraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,284 copying MDTraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,286 copying MDTraj/testing/reference/lysozyme-ligand-tripos.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,286 copying MDTraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,287 copying MDTraj/testing/reference/inpcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,289 copying MDTraj/testing/reference/imatinib.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,289 copying MDTraj/testing/reference/imatinib.mol2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,290 copying MDTraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,292 copying MDTraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,294 copying MDTraj/testing/reference/freesolve_v0.3.tar.bz2 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,296 copying MDTraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,297 copying MDTraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,298 copying MDTraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,300 copying MDTraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,304 copying MDTraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,306 copying MDTraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,309 copying MDTraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,311 copying MDTraj/testing/reference/frame0.lammpstrj -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,313 copying MDTraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,314 copying MDTraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,316 copying MDTraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,317 copying MDTraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,318 copying MDTraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,319 copying MDTraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,320 copying MDTraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,321 copying MDTraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,321 copying MDTraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,322 copying MDTraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,323 copying MDTraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,324 copying MDTraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,324 copying MDTraj/testing/reference/alanine.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,325 copying MDTraj/testing/reference/alanine-dipeptide-implicit.prmtop -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,326 copying MDTraj/testing/reference/alanine-dipeptide-explicit.prmtop -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,328 copying MDTraj/testing/reference/alanine-dipeptide-explicit.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,329 copying MDTraj/testing/reference/alanine-dipeptide-explicit.binpos -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,330 copying MDTraj/testing/reference/ala_dipeptide.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,332 copying MDTraj/testing/reference/ala_dipeptide.dcd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,333 copying MDTraj/testing/reference/ala_ala_ala.xpsf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,333 copying MDTraj/testing/reference/ala_ala_ala.psf -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,334 copying MDTraj/testing/reference/ala_ala_ala.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,335 copying MDTraj/testing/reference/ala_ala_ala.mdcrd -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,335 copying MDTraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,336 copying MDTraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,337 copying MDTraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,338 copying MDTraj/testing/reference/3nch.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,341 copying MDTraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,344 copying MDTraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,352 copying MDTraj/testing/reference/1vii.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,353 copying MDTraj/testing/reference/1vii.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,353 copying MDTraj/testing/reference/1ncw.pdb.gz -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,355 copying MDTraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,356 copying MDTraj/testing/reference/1am7_uncorrected.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,358 copying MDTraj/testing/reference/1am7_protein.pdb -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,360 copying MDTraj/testing/reference/1am7_corrected.xtc -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference 2025-09-08T00:47:02,362 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T00:47:02,363 copying MDTraj/testing/reference/ala_dipeptide_trj/timekeys -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T00:47:02,363 copying MDTraj/testing/reference/ala_dipeptide_trj/metadata -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T00:47:02,364 copying MDTraj/testing/reference/ala_dipeptide_trj/frame000000002 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T00:47:02,365 copying MDTraj/testing/reference/ala_dipeptide_trj/frame000000001 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T00:47:02,366 copying MDTraj/testing/reference/ala_dipeptide_trj/frame000000000 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T00:47:02,367 copying MDTraj/testing/reference/ala_dipeptide_trj/clickme.dtr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/ala_dipeptide_trj 2025-09-08T00:47:02,367 creating build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T00:47:02,367 copying MDTraj/testing/reference/frame0.dtr/timekeys -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T00:47:02,368 copying MDTraj/testing/reference/frame0.dtr/metadata -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T00:47:02,369 copying MDTraj/testing/reference/frame0.dtr/frame000000001 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T00:47:02,374 copying MDTraj/testing/reference/frame0.dtr/frame000000000 -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T00:47:02,378 copying MDTraj/testing/reference/frame0.dtr/clickme.dtr -> build/lib.linux-armv7l-cpython-313/mdtraj/testing/reference/frame0.dtr 2025-09-08T00:47:02,379 creating build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T00:47:02,379 copying MDTraj/html/static/widget_trajectory.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T00:47:02,380 copying MDTraj/html/static/widget_imagebutton.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T00:47:02,381 copying MDTraj/html/static/surface.min.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T00:47:02,382 copying MDTraj/html/static/objexporter.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T00:47:02,382 copying MDTraj/html/static/iview.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T00:47:02,383 copying MDTraj/html/static/filesaver.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T00:47:02,384 copying MDTraj/html/static/context.js -> build/lib.linux-armv7l-cpython-313/mdtraj/html/static 2025-09-08T00:47:02,385 creating build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T00:47:02,385 copying MDTraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T00:47:02,386 copying MDTraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-cpython-313/mdtraj/formats/pdb/data 2025-09-08T00:47:02,392 running build_ext 2025-09-08T00:47:02,393 building 'mdtraj.formats.xtc' extension 2025-09-08T00:47:02,395 creating build/temp.linux-armv7l-cpython-313/MDTraj/formats/xtc/src 2025-09-08T00:47:02,396 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -IMDTraj/formats/xtc -IMDTraj/formats/xtc/include/ -IMDTraj/formats/xtc/ -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c MDTraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-cpython-313/MDTraj/formats/xtc/src/xdrfile.o 2025-09-08T00:47:02,545 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2025-09-08T00:47:02,546 MDTraj/formats/xtc/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T00:47:02,546 495 | while (size >= num && num_of_bits < 32) 2025-09-08T00:47:02,546 | ^~ 2025-09-08T00:47:02,547 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2025-09-08T00:47:02,547 MDTraj/formats/xtc/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T00:47:02,547 541 | while (bytes[num_of_bytes] >= num) 2025-09-08T00:47:02,548 | ^~ 2025-09-08T00:47:02,549 MDTraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2025-09-08T00:47:02,550 MDTraj/formats/xtc/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T00:47:02,550 650 | if (num_of_bits >= num_of_bytes * 8) 2025-09-08T00:47:02,550 | ^~ 2025-09-08T00:47:02,551 MDTraj/formats/xtc/src/xdrfile.c:652:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T00:47:02,551 652 | for (i = 0; i < num_of_bytes; i++) 2025-09-08T00:47:02,551 | ^ 2025-09-08T00:47:02,552 MDTraj/formats/xtc/src/xdrfile.c:660:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T00:47:02,553 660 | for (i = 0; i < num_of_bytes-1; i++) 2025-09-08T00:47:02,553 | ^ 2025-09-08T00:47:02,554 MDTraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2025-09-08T00:47:02,555 MDTraj/formats/xtc/src/xdrfile.c:700:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T00:47:02,555 700 | if (lastbits < num_of_bits) 2025-09-08T00:47:02,555 | ^ 2025-09-08T00:47:02,557 MDTraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2025-09-08T00:47:02,558 MDTraj/formats/xtc/src/xdrfile.c:815:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T00:47:02,558 815 | if(size3>xfp->buf1size) 2025-09-08T00:47:02,558 | ^ 2025-09-08T00:47:02,560 MDTraj/formats/xtc/src/xdrfile.c:869:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T00:47:02,560 869 | maxidx = (LASTIDX size3) 2025-09-08T00:47:02,563 | ^ 2025-09-08T00:47:02,564 MDTraj/formats/xtc/src/xdrfile.c:788:32: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable] 2025-09-08T00:47:02,565 788 | int smallnum, smaller, larger, i, is_smaller, run; 2025-09-08T00:47:02,565 | ^~~~~~ 2025-09-08T00:47:02,565 MDTraj/formats/xtc/src/xdrfile.c:785:23: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable] 2025-09-08T00:47:02,565 785 | int smallidx, minidx, maxidx; 2025-09-08T00:47:02,565 | ^~~~~~ 2025-09-08T00:47:02,566 MDTraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2025-09-08T00:47:02,566 MDTraj/formats/xtc/src/xdrfile.c:1027:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T00:47:02,567 1027 | if(size3>xfp->buf1size) 2025-09-08T00:47:02,567 | ^ 2025-09-08T00:47:02,572 MDTraj/formats/xtc/src/xdrfile.c:1150:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T00:47:02,572 1150 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2025-09-08T00:47:02,573 | ^ 2025-09-08T00:47:02,573 MDTraj/formats/xtc/src/xdrfile.c:1156:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T00:47:02,573 1156 | maxidx = (LASTIDXxfp->buf1size) 2025-09-08T00:47:02,582 | ^ 2025-09-08T00:47:02,584 MDTraj/formats/xtc/src/xdrfile.c:1383:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T00:47:02,584 1383 | maxidx = (LASTIDXxfp->buf1size) { 2025-09-08T00:47:02,593 | ^ 2025-09-08T00:47:02,600 MDTraj/formats/xtc/src/xdrfile.c:1634:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-08T00:47:02,600 1634 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2025-09-08T00:47:02,601 | ^ 2025-09-08T00:47:02,602 MDTraj/formats/xtc/src/xdrfile.c:1639:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-08T00:47:02,602 1639 | maxidx = (LASTIDXn_frames == -1L); 2025-09-08T00:47:06,941 | ^~ 2025-09-08T00:47:06,976 MDTraj/formats/xtc/xtc.c:13062:12: error: implicit declaration of function ‘read_xtc_nframes’; did you mean ‘read_xtc_natoms’? [-Wimplicit-function-declaration] 2025-09-08T00:47:06,977 13062 | (void)(read_xtc_nframes(__pyx_t_6, (&__pyx_v_self->n_frames))); 2025-09-08T00:47:06,977 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:47:06,977 | read_xtc_natoms 2025-09-08T00:47:08,512 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T00:47:08,715 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T00:47:08,729 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T00:47:08,729 exec(compile('"'"''"'"''"'"' 2025-09-08T00:47:08,729 # This is -- a caller that pip uses to run setup.py 2025-09-08T00:47:08,729 # 2025-09-08T00:47:08,729 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T00:47:08,729 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T00:47:08,729 # - It provides a clear error message when setuptools is not installed. 2025-09-08T00:47:08,729 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T00:47:08,729 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T00:47:08,729 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T00:47:08,729 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T00:47:08,729 import os, sys, tokenize, traceback 2025-09-08T00:47:08,729 2025-09-08T00:47:08,729 try: 2025-09-08T00:47:08,729 import setuptools 2025-09-08T00:47:08,729 except ImportError: 2025-09-08T00:47:08,729 print( 2025-09-08T00:47:08,729 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T00:47:08,729 "the build environment with exception:", 2025-09-08T00:47:08,729 file=sys.stderr, 2025-09-08T00:47:08,729 ) 2025-09-08T00:47:08,729 traceback.print_exc() 2025-09-08T00:47:08,729 sys.exit(1) 2025-09-08T00:47:08,729 2025-09-08T00:47:08,729 __file__ = %r 2025-09-08T00:47:08,729 sys.argv[0] = __file__ 2025-09-08T00:47:08,729 2025-09-08T00:47:08,729 if os.path.exists(__file__): 2025-09-08T00:47:08,729 filename = __file__ 2025-09-08T00:47:08,729 with tokenize.open(__file__) as f: 2025-09-08T00:47:08,729 setup_py_code = f.read() 2025-09-08T00:47:08,729 else: 2025-09-08T00:47:08,729 filename = "" 2025-09-08T00:47:08,729 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T00:47:08,729 2025-09-08T00:47:08,729 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T00:47:08,729 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-tzknklh8/mdtraj_b63165ccb7e44ef6ba1d0d71db467c96/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-1lk86_zm[/] 2025-09-08T00:47:08,729 [bold magenta]cwd[/]: /tmp/pip-wheel-tzknklh8/mdtraj_b63165ccb7e44ef6ba1d0d71db467c96/ 2025-09-08T00:47:08,729 Building wheel for mdtraj (setup.py): finished with status 'error' 2025-09-08T00:47:08,730 ERROR: Failed building wheel for mdtraj 2025-09-08T00:47:08,731 Running setup.py clean for mdtraj 2025-09-08T00:47:08,732 Running command python setup.py clean 2025-09-08T00:47:09,714 C compiler: 2025-09-08T00:47:09,719 Using built-in specs. 2025-09-08T00:47:09,719 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-08T00:47:09,719 COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/14/lto-wrapper 2025-09-08T00:47:09,719 Target: arm-linux-gnueabihf 2025-09-08T00:47:09,719 Configured with: ../src/configure -v --with-pkgversion='Raspbian 14.2.0-19+rpi1' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --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-libstdcxx-backtrace --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+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2025-09-08T00:47:09,720 Thread model: posix 2025-09-08T00:47:09,720 Supported LTO compression algorithms: zlib zstd 2025-09-08T00:47:09,720 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-08T00:47:11,199 Attempting to autodetect OpenMP support... Did not detect OpenMP support 2025-09-08T00:47:11,876 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2025-09-08T00:47:12,831 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2025-09-08T00:47:14,036 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T00:47:14,036 !! 2025-09-08T00:47:14,036 ******************************************************************************** 2025-09-08T00:47:14,036 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T00:47:14,037 License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+) 2025-09-08T00:47:14,037 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T00:47:14,037 ******************************************************************************** 2025-09-08T00:47:14,037 !! 2025-09-08T00:47:14,037 self._finalize_license_expression() 2025-09-08T00:47:14,124 running clean 2025-09-08T00:47:14,296 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T00:47:14,297 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T00:47:14,311 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T00:47:14,311 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T00:47:14,311 removing 'build' 2025-09-08T00:47:14,508 Failed to build mdtraj 2025-09-08T00:47:14,509 ERROR: Failed to build one or more wheels 2025-09-08T00:47:14,510 Exception information: 2025-09-08T00:47:14,510 Traceback (most recent call last): 2025-09-08T00:47:14,510 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T00:47:14,510 status = _inner_run() 2025-09-08T00:47:14,510 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T00:47:14,510 return self.run(options, args) 2025-09-08T00:47:14,510 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T00:47:14,510 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T00:47:14,510 return func(self, options, args) 2025-09-08T00:47:14,510 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T00:47:14,510 raise CommandError("Failed to build one or more wheels") 2025-09-08T00:47:14,510 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T00:47:14,514 Removed build tracker: '/tmp/pip-build-tracker-6i72_usq'