2021-07-10T09:34:18,042 Created temporary directory: /tmp/pip-ephem-wheel-cache-namszdu4
2021-07-10T09:34:18,044 Created temporary directory: /tmp/pip-req-tracker-mvoifg0p
2021-07-10T09:34:18,045 Initialized build tracking at /tmp/pip-req-tracker-mvoifg0p
2021-07-10T09:34:18,045 Created build tracker: /tmp/pip-req-tracker-mvoifg0p
2021-07-10T09:34:18,045 Entered build tracker: /tmp/pip-req-tracker-mvoifg0p
2021-07-10T09:34:18,046 Created temporary directory: /tmp/pip-wheel-m_grhd85
2021-07-10T09:34:18,075 1 location(s) to search for versions of mdtraj:
2021-07-10T09:34:18,075 * https://pypi.org/simple/mdtraj/
2021-07-10T09:34:18,075 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/
2021-07-10T09:34:18,076 Getting page https://pypi.org/simple/mdtraj/
2021-07-10T09:34:18,078 Found index url https://pypi.org/simple
2021-07-10T09:34:18,291   Found link https://files.pythonhosted.org/packages/cb/82/93ced2a2e5d37f36330fe3e74081fdd4ce8f933ebd16b4fab14cb5c6c29c/mdtraj-0.3.tar.gz#sha256=4cbd8bbeebacd0fae186244b817edd5dfd7546426fbe7bc2a80002644baa9b8a (from https://pypi.org/simple/mdtraj/), version: 0.3
2021-07-10T09:34:18,292   Found link https://files.pythonhosted.org/packages/bb/79/e0703632501b528c6d4fb87e672aa68e431579e61ddf15b9178554e45a8e/mdtraj-0.3.1.tar.gz#sha256=86d8b14ea7e8757475f32e346a05e7d8bb0e374d6c7b89a7d7fa9ba7f76acd09 (from https://pypi.org/simple/mdtraj/), version: 0.3.1
2021-07-10T09:34:18,292   Skipping link: unsupported archive format: .exe: https://files.pythonhosted.org/packages/76/8f/0e6b0243ec53f87b024e84b26b0ced2ca716dd347ac459ef5c65e887fd02/mdtraj-0.3.1.win-amd64-py2.7.exe#sha256=a1a15f2f5a5d840e5c790e28339c060839926ee18079567f90273c8f1f3ae064 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,292   Found link https://files.pythonhosted.org/packages/6e/2c/5e68a951b1d038ce32d5e0e128f56ee7ff0ea0ce933e7c05a2b9a2c56b9d/mdtraj-0.4.0.tar.gz#sha256=8eb89b88c3e900e0594ebbaff55c07a59959411a69c7e436933b899e81d7d3e4 (from https://pypi.org/simple/mdtraj/), version: 0.4.0
2021-07-10T09:34:18,293   Found link https://files.pythonhosted.org/packages/83/4d/820da3023ad7d89e3dfcdfca11a298ded20d99383f43ce2bdef30c120d8e/mdtraj-0.4.1.tar.gz#sha256=0b0e6c28aa596e442ea3763c7ffdcc6f714152c330b9b799b088f5c4bd8bd553 (from https://pypi.org/simple/mdtraj/), version: 0.4.1
2021-07-10T09:34:18,293   Found link https://files.pythonhosted.org/packages/c3/6d/3c211650aacc169d271d86de954d08f96b835e7f0d08de472cf7fe5b41b3/mdtraj-0.4.3.tar.gz#sha256=52699d9bc832ee42da60fdb7dc1348937339e75a56ebb384dc31b1f64c57b455 (from https://pypi.org/simple/mdtraj/), version: 0.4.3
2021-07-10T09:34:18,293   Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/d7/ad/6610b9029c85be5fe896b9a6d0bd6a7e960db1ec751ff7e6a36594eebd05/mdtraj-0.4.3.win32-py2.6.msi#sha256=fa4828c68e0bad725f4f82dce6fda7ea482307b6a3e2dc57365320973b3b4ec7 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,293   Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/f2/d0/2ea0d56c38693e121a8b646a688cbb3f7d1d5d5dc3a89893e358e70cf4e3/mdtraj-0.4.3.win32-py2.7.msi#sha256=c382d9baff2c2bbcc7368b85729643016efcb990dee7ab46c9124895d10a6c0f (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,294   Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/c5/fa/7f4579a0eb11ea6eab4cf94a0b10ca9bebdeeee53e022ad7a66d7a3c5dfb/mdtraj-0.4.3.win32-py3.2.msi#sha256=c61705d67927947a286ba9c7c39a3f82ea24ecbee5ab52a2f75adb6dd2dfd0a5 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,294   Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/28/e5/cb27f0a2b7a3c604704fe9fa92d8b3f5e82bd3a5a50f17548d79875618d7/mdtraj-0.4.3.win32-py3.3.msi#sha256=0b2a969e3ccf22825fceeaaf2acedc7b1ab0efd44f88b3262feae66bb246e6d4 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,294   Found link https://files.pythonhosted.org/packages/e5/88/d95a7bf9ab9f170c4a765b24aef3249f8b48419eb8200c0e6e0cefb8df27/mdtraj-0.4.3.zip#sha256=183b42cb33c97ffc8321eea42a8f9bf1dc8daf70fcd77ed1a2f010ceb1aa6ddc (from https://pypi.org/simple/mdtraj/), version: 0.4.3
2021-07-10T09:34:18,294   Found link https://files.pythonhosted.org/packages/d7/77/493f388512cb4e90e787ed60e206b053c4999f59ea8e473f182c041e7bb5/mdtraj-0.5.0.tar.gz#sha256=067baaef07eccfc5d5b4d0cd4bb18f92fb23bf405b42a650443fe32c1b24ed7b (from https://pypi.org/simple/mdtraj/), version: 0.5.0
2021-07-10T09:34:18,295   Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/0e/5a/a74bf3100d9fa5ff67cf6b271c8ad0254402f96f68da5b4015bdd62313fd/mdtraj-0.5.0.win32-py2.7.msi#sha256=c339f8245f776be3e62e1ce480afc14757c371137c127e3658bd0f4eba4176e3 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,295   Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/58/b4/71dae8ecfac23b90e0bbcbcb21bc3770277d42717e7476cc6502b07a2b35/mdtraj-0.5.0.win32-py3.2.msi#sha256=b65fe9caef8a65d1431bf14b0440eff07b53ecec00908a2254050778e2a69f1c (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,295   Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/16/bc/e7b082171abfe965d04cfafd5851541644c0cb831a6a2a24167986cd1fe1/mdtraj-0.5.0.win32-py3.3.msi#sha256=5f9af92b3f1cd50e8cbeb5ede2f35175d8e66f081b0dccc9f828209e2c649ece (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,295   Found link https://files.pythonhosted.org/packages/f3/91/344c3301a96d586b7280b9fcc70c59a804df499219f0fbb750c8b2bfb818/mdtraj-0.5.0.zip#sha256=7f675810a15632557b6974402b52c2a317f65e4aefb21cc4fb9e5f59c2a6a035 (from https://pypi.org/simple/mdtraj/), version: 0.5.0
2021-07-10T09:34:18,296   Found link https://files.pythonhosted.org/packages/0f/d3/df89fa19d0572c58f82e17d57a1409cefb7525b0c96930876f42563bc937/mdtraj-0.5.1.tar.gz#sha256=bbfe583ffc3026d8125a99776aafaccc64af6f2b11d26372c025cc33dc5266ec (from https://pypi.org/simple/mdtraj/), version: 0.5.1
2021-07-10T09:34:18,296   Found link https://files.pythonhosted.org/packages/07/17/04c7422cc1092ca74b51da1f9ba4f76e38b53ef6f35bf4ad4bb65301c316/mdtraj-0.5.1.zip#sha256=258a81b7b500493e36ea590f7222ae06df4782a6d5de4d04a3569a831a98584b (from https://pypi.org/simple/mdtraj/), version: 0.5.1
2021-07-10T09:34:18,296   Found link https://files.pythonhosted.org/packages/59/41/0768b99fcb72f568950c767a0866b92d9a328f9b3c848e3f0f6426c49bc7/mdtraj-0.6.0.tar.gz#sha256=e5b41177be9a6f3527b6af210dc70e36607dde8cd525cd40ebe1c002d69c98a5 (from https://pypi.org/simple/mdtraj/), version: 0.6.0
2021-07-10T09:34:18,297   Found link https://files.pythonhosted.org/packages/85/33/c0708f41cc090a886342325cb99db876b555a181ee18a3a1086b1b87dfd1/mdtraj-0.6.0.zip#sha256=7ebfc1a1249d973f203f6e141211cdb1c5fa8a43f7058f19304d0269378edccc (from https://pypi.org/simple/mdtraj/), version: 0.6.0
2021-07-10T09:34:18,297   Found link https://files.pythonhosted.org/packages/b1/b4/6219cf2656a223f06d3e40d5098fa186aba73ac5d3cbb08348fa73bf0c7e/mdtraj-0.6.1.tar.gz#sha256=e38d3b2c742c01014e57f83d3f6ddfe00e8dac95730d3335f3f3a715c8f9188a (from https://pypi.org/simple/mdtraj/), version: 0.6.1
2021-07-10T09:34:18,297   Found link https://files.pythonhosted.org/packages/59/3e/3184bc16bbf5f14ea3148552ae43ebfb28e3abc6ea08a76e3e31b81f938a/mdtraj-0.6.1.zip#sha256=49bb8956ce3bc8f43dfb7fdf0897217a2e170cb7180311951c323af62aee3388 (from https://pypi.org/simple/mdtraj/), version: 0.6.1
2021-07-10T09:34:18,297   Found link https://files.pythonhosted.org/packages/2d/7b/67e57aeabcd1383fac5d169f866836e00410a41f6311d4c3e1d809a9c9e8/mdtraj-0.7.0.tar.gz#sha256=3a2ba2cf422c636ad743f6e1d6b2b75c7830788f78d37e0749a49ef311919c55 (from https://pypi.org/simple/mdtraj/), version: 0.7.0
2021-07-10T09:34:18,298   Found link https://files.pythonhosted.org/packages/bb/31/a472847da32caa824a73c3794f5816005b2a213f6c35df20dc55d1d07be8/mdtraj-0.7.0.zip#sha256=b45210e1d7eabdb9ff30338bcbbbc6d7624720ddd7d76c9ceb88f2baaaa5289f (from https://pypi.org/simple/mdtraj/), version: 0.7.0
2021-07-10T09:34:18,298   Found link https://files.pythonhosted.org/packages/3a/f1/de324881e0c838b8eda4222a02ac5b0595e52c40225046a67e845db5fb35/mdtraj-0.8.0.tar.gz#sha256=1d931c45e0bb258211d820b222ea0be23f03339f6057e1b9d5845283a406c1f3 (from https://pypi.org/simple/mdtraj/), version: 0.8.0
2021-07-10T09:34:18,298   Found link https://files.pythonhosted.org/packages/d8/87/01f61e5cabbf391ed20ec15854454f7bd76d752413be983654c2de738292/mdtraj-0.8.0.zip#sha256=d255f9f0509205109aa08a853fdb004cac9e8075b5ba370d17903519ff7c0f39 (from https://pypi.org/simple/mdtraj/), version: 0.8.0
2021-07-10T09:34:18,299   Found link https://files.pythonhosted.org/packages/77/72/4f559e05820f485e2f1542154660ed9746e4822a097022ab79a5afba53a1/mdtraj-0.9.0.tar.gz#sha256=cf0603b650e5564a0ec885f19c5c112aeedb2f9918260d39e49ddc52558d2085 (from https://pypi.org/simple/mdtraj/), version: 0.9.0
2021-07-10T09:34:18,299   Skipping link: unsupported archive format: .msi: https://files.pythonhosted.org/packages/48/71/d6bf7c8e7fa50e826a16c89bf00aa636953aa6efa462d01f04543f51536d/mdtraj-0.9.0.win32-py2.7.msi#sha256=cdd6201437a8c06dc75844af7710c26fc2ebe1984bb80448bafec946ca744599 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,299   Found link https://files.pythonhosted.org/packages/5a/a4/ab877500acc0e0b953d8ffa8de21719fcbb78749c2fd682f82601a0f3a3d/mdtraj-0.9.0.zip#sha256=dcc380dbcea821f50bceb6f3492d46122a6b15336a12cb50cd49d31d9700e687 (from https://pypi.org/simple/mdtraj/), version: 0.9.0
2021-07-10T09:34:18,299   Found link https://files.pythonhosted.org/packages/de/4b/cb27df1a4b50e52cbbd33d8e123d3f252e108a263a8389a8297e5810b453/mdtraj-1.0.0.tar.gz#sha256=13ad540294bab66f794a16e4c703297e3c0a35b5ea6a62d569d69ce98e25341f (from https://pypi.org/simple/mdtraj/), version: 1.0.0
2021-07-10T09:34:18,300   Found link https://files.pythonhosted.org/packages/8e/36/9fd92ca45c2b84384f78020524edb9dfd2d4cefc0595472cc60b64af62ed/mdtraj-1.0.0.zip#sha256=8aa8e04038453b3201d906e1ecb01cb4261f0e9230d72e62786255f68e09d86d (from https://pypi.org/simple/mdtraj/), version: 1.0.0
2021-07-10T09:34:18,300   Found link https://files.pythonhosted.org/packages/dd/e2/b7a137d7bff0dba7347d3ad2462e811bdcfc8de0bc3f6b78f93c2af78a58/mdtraj-1.1.0.tar.gz#sha256=ff1b089b9231b17de27f1f4d1eb6298129351269eca290381fdc06977edee37a (from https://pypi.org/simple/mdtraj/), version: 1.1.0
2021-07-10T09:34:18,300   Found link https://files.pythonhosted.org/packages/13/c2/b758f772bbf35fe8069509d59c701de491f2cf3c9b63658e4ddc3cfcf468/mdtraj-1.1.0.zip#sha256=fc842a7adf741036580c82afae83dab547578bd6dd59d3e93956d8a0fd5e07ad (from https://pypi.org/simple/mdtraj/), version: 1.1.0
2021-07-10T09:34:18,317   Skipping link: none of the wheel's tags (cp27-none-win32) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1e/bc/4d4fd31a09fbed9d2e1e6a90fa0657e5c22f40b9ae542f932854b20b867a/mdtraj-1.2.0-cp27-none-win32.whl#sha256=43ea879b8772eed171d7244a9feb5f04da3e7c902e8a7d1aac12a3de67a9df89 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,318   Skipping link: none of the wheel's tags (cp33-none-win32) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/59/d7/f4809991e14a568656957523111763cd3105ad3f63d53b470643f3c391c7/mdtraj-1.2.0-cp33-none-win32.whl#sha256=af120862f79ea4bebcbf3f246a0336ebe23f0ecda7a484f52db999a86eb0091e (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,318   Skipping link: none of the wheel's tags (cp34-none-win32) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/47/ec/0da56abb0793e6c03ca647bb66a01e175e9cd80623b77cc3eee7aa4b0169/mdtraj-1.2.0-cp34-none-win32.whl#sha256=e4fbe22ffbcebc9f7695b0cbab441cc04ad6c998ac3232bb1156c45934b89bfa (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,319   Found link https://files.pythonhosted.org/packages/b9/7d/a2878b6c3da5e04ad15f906235bbf6507d5b801465b6a7626cd7f6e33289/mdtraj-1.2.0.tar.gz#sha256=7dff42a449a4858ab5db9b7f1528ae314b0d98c6ebd432307de4f14be6f446e0 (from https://pypi.org/simple/mdtraj/), version: 1.2.0
2021-07-10T09:34:18,319   Found link https://files.pythonhosted.org/packages/ad/60/131151a1dacdf1fb8aa2afb20d2f7865802ee8a654f5c46bf0990cd44b77/mdtraj-1.2.0.zip#sha256=b6e930608c366b86ff6523485264788caf12b7f5c8be369bbc98ee31d569551e (from https://pypi.org/simple/mdtraj/), version: 1.2.0
2021-07-10T09:34:18,319   Found link https://files.pythonhosted.org/packages/19/43/14b0d39a19b9bf7129c1d1c00fb3ef6b201dd6ca26d4b5d82e06d5523931/mdtraj-1.3.0.tar.gz#sha256=233089791c6fbe00f6208ca412a09c1353a755866311ca3e663a1193ecbfe342 (from https://pypi.org/simple/mdtraj/), version: 1.3.0
2021-07-10T09:34:18,320   Found link https://files.pythonhosted.org/packages/52/1c/5241b6d7eedc4d1c17a5b87665216f5781efdd7b3ad742fec151ca5db5f8/mdtraj-1.3.0.zip#sha256=7be7a99823c08ef93f01483815774c0ac9aefd8c3790d0f9069fe6685bf3a45b (from https://pypi.org/simple/mdtraj/), version: 1.3.0
2021-07-10T09:34:18,320   Found link https://files.pythonhosted.org/packages/97/1c/bce6eb773069063889ddf3969cdbd547697cca8909de4a285721bd4b936c/mdtraj-1.4.0.tar.gz#sha256=26fc6c481cb472e66238542f6071d53fba45ff7fd542914b53fea2bb28c8f272 (from https://pypi.org/simple/mdtraj/), version: 1.4.0
2021-07-10T09:34:18,320   Found link https://files.pythonhosted.org/packages/20/4d/0fdff16d6d1b9a1e1e0d6f0391226c2a0791810e07772fa7e3b6713e5c9a/mdtraj-1.4.0.zip#sha256=6337fe3cc50c9ad1c745019e84175dd3c56b108b7f3000e1296549969c6916de (from https://pypi.org/simple/mdtraj/), version: 1.4.0
2021-07-10T09:34:18,320   Found link https://files.pythonhosted.org/packages/37/bb/c7261dd1fc35105898af6de578719e8eb18aa33f70dd38a4257ff68118c4/mdtraj-1.4.1.tar.gz#sha256=8ada69d633ef93baf2dbfd572881343e7373616720087dd2d7767e4c371c17ac (from https://pypi.org/simple/mdtraj/), version: 1.4.1
2021-07-10T09:34:18,321   Found link https://files.pythonhosted.org/packages/eb/b4/4fd2c5d63e4a1f10047df8a3f83071d41ba9203abf1a86d381f2c16cef94/mdtraj-1.4.1.zip#sha256=b58cb4ff9cc191871b06d71768128584753a8136d09cd8ff5445da333bc283c9 (from https://pypi.org/simple/mdtraj/), version: 1.4.1
2021-07-10T09:34:18,321   Found link https://files.pythonhosted.org/packages/af/43/7594de45f455b32c5a057bc323336461a7f4299a5e93dfb57038e0c7c99c/mdtraj-1.4.2.tar.gz#sha256=7a1fa2ba877193f7d99d8c2fd9b0200fb124c8a2fbcbfa4e701a8b52718fa6a0 (from https://pypi.org/simple/mdtraj/), version: 1.4.2
2021-07-10T09:34:18,321   Found link https://files.pythonhosted.org/packages/79/d7/7ec8477e4293f027acd7695ae8d493eb7985aec5666ce3d117d48794fa5c/mdtraj-1.4.2.zip#sha256=dc1c31b956ad5e88590048abaaaa33bad58887262e94e2921c070d9e6d5fd5df (from https://pypi.org/simple/mdtraj/), version: 1.4.2
2021-07-10T09:34:18,322   Found link https://files.pythonhosted.org/packages/f8/36/a0a83efc5f48db485bdefd15a7ade8a80876bbe178318cfa14ced3cb0c87/mdtraj-1.5.0.tar.gz#sha256=08a9af719ecd4754f12e41031485c5820bf4a51371909e4f0060d96e4998c265 (from https://pypi.org/simple/mdtraj/), version: 1.5.0
2021-07-10T09:34:18,322   Found link https://files.pythonhosted.org/packages/b2/2c/1cfc1f7879ea82293afca1edd595f3ca39e25f8411627175e88ea6819f83/mdtraj-1.5.0.zip#sha256=e56dcf4b7be97c007692b6c6758f8fc8b84811e666de1c3836631e697dab9394 (from https://pypi.org/simple/mdtraj/), version: 1.5.0
2021-07-10T09:34:18,322   Skipping link: none of the wheel's tags (cp27-none-macosx_10_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/a8/24/4c267bc9753b3d1218b1d9c9220d3811d71eea2cfba590f512bcbb2a9c3b/mdtraj-1.5.1-cp27-none-macosx_10_5_x86_64.whl#sha256=0f9e97389fcf01c60984b7a33b04529ea440d5a79bad90ee8781de33c27fb9a0 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,323   Skipping link: none of the wheel's tags (cp34-cp34m-macosx_10_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/5e/07/f6d8703864e39672cb420701e6a8ef0c2d3000e9b0bcc25777d29d526350/mdtraj-1.5.1-cp34-cp34m-macosx_10_5_x86_64.whl#sha256=9554b9bcb0729d9dbc10b9ccc74506544a2c2e37d4a478f83fd8d1cba081b2d7 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,323   Skipping link: none of the wheel's tags (cp35-cp35m-macosx_10_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/2b/6e/a791501a9a60b3cb2063fc3db8d4d9b1a27cfa4432261b98f804f9bf34e1/mdtraj-1.5.1-cp35-cp35m-macosx_10_5_x86_64.whl#sha256=a8e1eafa532abd1165e5e15636faf0c0858ab03239dbf8264ad23ac1bd820f13 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,323   Found link https://files.pythonhosted.org/packages/dc/6c/2173608f090cf361b8c858e7db974757a8ec9c639ce69b100e9a4608875e/mdtraj-1.5.1.tar.gz#sha256=15d57e229e5be9ba2b4a78d004bf57ae63ba5e86079b47643654751faf41e014 (from https://pypi.org/simple/mdtraj/), version: 1.5.1
2021-07-10T09:34:18,324   Found link https://files.pythonhosted.org/packages/78/ae/82df7eca71fa9e71ad4638f8c222164ccc3583874cb4a6875a04586312bc/mdtraj-1.5.1.zip#sha256=d97591eebf1e9ae04c2b2e144340a959ed359fe33037c647b174f017bab482c3 (from https://pypi.org/simple/mdtraj/), version: 1.5.1
2021-07-10T09:34:18,324   Found link https://files.pythonhosted.org/packages/40/21/40aeb64c81f480e07b1e1c31c6b3b332bc38df08d5fd30210fc235acdb3d/mdtraj-1.6.0.tar.gz#sha256=6da885f0f3bad7baa27adf6f7cac62282e02e58b319144f1fefeaa6d3ca8fe7a (from https://pypi.org/simple/mdtraj/), version: 1.6.0
2021-07-10T09:34:18,324   Found link https://files.pythonhosted.org/packages/8f/9e/cf5814ce6a29a474dc2b61492ed36dde1397b1707e63248bafe495529c29/mdtraj-1.6.0.zip#sha256=9d281e43cbc7133615dc0b81e63f64e79e39e3d25098103798301f3c06383c0b (from https://pypi.org/simple/mdtraj/), version: 1.6.0
2021-07-10T09:34:18,325   Found link https://files.pythonhosted.org/packages/a7/09/abb145901e09665d3a7931527e34a160049cebf4eba3506a69db2093f5f9/mdtraj-1.6.1.tar.gz#sha256=1d390acb7bbe09c7a2b1c639c641c47eef09c37bd525cd83c201addda37074c8 (from https://pypi.org/simple/mdtraj/), version: 1.6.1
2021-07-10T09:34:18,325   Found link https://files.pythonhosted.org/packages/38/44/179f101e32ab7ceb52864fb4ef2955c0807b9f548c087f39f2cfd18cb498/mdtraj-1.6.1.zip#sha256=bca98c6339d04b36934b37857eae9f42fb667e1745d4d7dc29ebfd4e3c653365 (from https://pypi.org/simple/mdtraj/), version: 1.6.1
2021-07-10T09:34:18,325   Found link https://files.pythonhosted.org/packages/bf/81/6f611041374bd7d2d49a15040d999cc52eed1a44e856a4a8d9c02370ac37/mdtraj-1.7.2.tar.gz#sha256=1bc9fb06e84f6562e51e040946dae0b940eaca4760f78f3ac451f4a89b132a9a (from https://pypi.org/simple/mdtraj/), version: 1.7.2
2021-07-10T09:34:18,325   Found link https://files.pythonhosted.org/packages/ff/b2/8785a8c9c7119e1a7c4e64072ccf428f75a3b0a9782a7ac25e5402b0a59d/mdtraj-1.7.2.zip#sha256=3158176cd2c21d2abdff5b2cbd9cac323f337b831123d5201bbb7d3fbe69e714 (from https://pypi.org/simple/mdtraj/), version: 1.7.2
2021-07-10T09:34:18,326   Found link https://files.pythonhosted.org/packages/cd/9f/027fa58d4e93dd3d700e22d5766961c970f6882c2bffd33daef55219d078/mdtraj-1.8.0.tar.gz#sha256=480fa4c280146e91db0ab7811f6fba5da29e89452b071d366a8e68247a88ffea (from https://pypi.org/simple/mdtraj/), version: 1.8.0
2021-07-10T09:34:18,326   Found link https://files.pythonhosted.org/packages/4a/2e/5bb01aaa8cd2ea9d75dd2ac12fd9f04f7137a8c996bde0138ad1b5e54ecb/mdtraj-1.8.0.zip#sha256=867325cb206dca4a605de4877e17e5e1983f2e778a6ef64594bd4250142561a8 (from https://pypi.org/simple/mdtraj/), version: 1.8.0
2021-07-10T09:34:18,326   Found link https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz#sha256=ca1ae07c5f5ce59940a48388ac9b098f8e22743b5f3ed3f46d5e3d1317b06282 (from https://pypi.org/simple/mdtraj/), version: 1.9.1
2021-07-10T09:34:18,327   Found link https://files.pythonhosted.org/packages/e0/9e/857f613eae8af3fb8cc73904b3edf622c58de3884c5989e4466973c3c9ee/mdtraj-1.9.2.tar.gz#sha256=cdd926f19c007955f0f768d36d696f3e77b4c8030289a2b40eb97a91cebacd0f (from https://pypi.org/simple/mdtraj/), version: 1.9.2
2021-07-10T09:34:18,327   Found link https://files.pythonhosted.org/packages/72/68/1efc74927df6fdaaa4816556a2534f4560cb69ed573ccac728e4fb8e3e09/mdtraj-1.9.3.tar.gz#sha256=5d95e045b1dd093a26bf6fea9895c3c6b52955d8f7fceee867a519ccf29640b3 (from https://pypi.org/simple/mdtraj/), version: 1.9.3
2021-07-10T09:34:18,327   Found link https://files.pythonhosted.org/packages/50/1d/581a080a1900f61bb1c0388e29517a54d4034faa094d40d794e1f96597d9/mdtraj-1.9.4.tar.gz#sha256=d5d28be24dd5f38e8b272c3a445a6cdbffc374b30e891c5535f65bb20f7e8b24 (from https://pypi.org/simple/mdtraj/), version: 1.9.4
2021-07-10T09:34:18,328   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1b/77/3ac1597812fc28964662587d405f85986206192623b434f7d0fa1b4a6a5b/mdtraj-1.9.5-cp36-cp36m-manylinux1_x86_64.whl#sha256=c02a9a589acc98dd3cc4db9b0cb21725f5e2cb9484c14cc4fa032a4663c7a1e9 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,328   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/af/da/271e93bb98bc93ccac17bc1f31f814be4f9e7024ac19bf31af892a462030/mdtraj-1.9.5-cp37-cp37m-manylinux1_x86_64.whl#sha256=8816f9a91826e46a413fd1a5ffd663b4076cf4c3b8930bb2046814d1438a88ee (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,329   Skipping link: none of the wheel's tags (cp38-cp38-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/3b/fd/4ffba665d0b0346072f61d0e8ef7ab281202db445d99136c717c89169a97/mdtraj-1.9.5-cp38-cp38-manylinux1_x86_64.whl#sha256=84bb3ced0ff61c4b3b38a36d71837599f50c8723c5d9e555dced51d0d09e10a1 (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,329   Skipping link: none of the wheel's tags (cp39-cp39-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/68/53/2f666107565f4735abd859b6af6867353eb08d0e9728d90fb0abc12d578e/mdtraj-1.9.5-cp39-cp39-manylinux1_x86_64.whl#sha256=7eae1adc6aa876396c9797d80db3f71da831601fb1739da731e1de9ca8ac96ab (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,329   Found link https://files.pythonhosted.org/packages/d8/cb/5dcc31c7e2c4485bd2aea66233def28954f2dc530607f5c43fefab71a963/mdtraj-1.9.5.tar.gz#sha256=f22c28c9dd51aa0f8692078dd3c2c7a338a7ca27cbd9aaeb669a60361e95adc4 (from https://pypi.org/simple/mdtraj/), version: 1.9.5
2021-07-10T09:34:18,330   Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64, cp36-cp36m-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/fe/a7/2a1392fe56ddd22a9cf5dcff7d684bdd7ce146d5c32839080dd8de7122dd/mdtraj-1.9.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=8d437742ec45ff619c7a50afacf16f3a791d604cd0be74b5b74d90b0dc3f577a (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,330   Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64, cp37-cp37m-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ce/ee/2015ff88cacb7c75b5e1cf6a57e8a089549b0e76bcd9474a08845f7ef12f/mdtraj-1.9.6-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=49f4251f83a7fdea4a8122369ef47f213bb1c1cfc38b91177e98985484fb63bf (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,331   Skipping link: none of the wheel's tags (cp38-cp38-manylinux1_x86_64, cp38-cp38-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c0/61/2fb002b9b2ab90567eb1a837ed510152ddadd5b8358ac800b591e37675e0/mdtraj-1.9.6-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=84bf863729d435df0dd1f86c3023cbe85b8940b102f9d6ef6ce00dcb9130883c (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,331   Skipping link: none of the wheel's tags (cp39-cp39-manylinux1_x86_64, cp39-cp39-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/09/49/85dc22a3c28108dfd0bce8a4268ae3937167b18fac531a0d801505cad7d9/mdtraj-1.9.6-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=44fcc435df4057126c123585e36a8a4563e24588ad438c916751e2e01501e2ff (from https://pypi.org/simple/mdtraj/)
2021-07-10T09:34:18,332   Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz#sha256=5b7c9b98dd0a1c1a2ddd6c1690fba6096a63314da2e79e05a8a1402b8949ad3c (from https://pypi.org/simple/mdtraj/), version: 1.9.6
2021-07-10T09:34:18,332 Skipping link: not a file: https://pypi.org/simple/mdtraj/
2021-07-10T09:34:18,340 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates
2021-07-10T09:34:18,359 Collecting mdtraj==1.5.0
2021-07-10T09:34:18,361   Created temporary directory: /tmp/pip-unpack-viwtw9q1
2021-07-10T09:34:19,079   Downloading mdtraj-1.5.0.zip (17.9 MB)
2021-07-10T09:34:23,005   Added mdtraj==1.5.0 from https://files.pythonhosted.org/packages/b2/2c/1cfc1f7879ea82293afca1edd595f3ca39e25f8411627175e88ea6819f83/mdtraj-1.5.0.zip#sha256=e56dcf4b7be97c007692b6c6758f8fc8b84811e666de1c3836631e697dab9394 to build tracker '/tmp/pip-req-tracker-mvoifg0p'
2021-07-10T09:34:23,006     Running setup.py (path:/tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/setup.py) egg_info for package mdtraj
2021-07-10T09:34:23,007     Created temporary directory: /tmp/pip-pip-egg-info-utat2acn
2021-07-10T09:34:23,007     Running command python setup.py egg_info
2021-07-10T09:34:23,933     Using built-in specs.
2021-07-10T09:34:23,934     COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc
2021-07-10T09:34:23,935     COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper
2021-07-10T09:34:23,935     Target: arm-linux-gnueabihf
2021-07-10T09:34:23,935     Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
2021-07-10T09:34:23,935     Thread model: posix
2021-07-10T09:34:23,935     Supported LTO compression algorithms: zlib zstd
2021-07-10T09:34:23,936     gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
2021-07-10T09:34:25,042     C compiler:
2021-07-10T09:34:25,043     Attempting to autodetect OpenMP support... Compiler supports OpenMP
2021-07-10T09:34:25,043     Attempting to autodetect SSE3   support... Did not detect SSE3 support
2021-07-10T09:34:25,043     Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support

2021-07-10T09:34:25,043     running egg_info
2021-07-10T09:34:25,045     creating /tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info
2021-07-10T09:34:25,046     writing /tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info/PKG-INFO
2021-07-10T09:34:25,048     writing dependency_links to /tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info/dependency_links.txt
2021-07-10T09:34:25,050     writing entry points to /tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info/entry_points.txt
2021-07-10T09:34:25,052     writing requirements to /tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info/requires.txt
2021-07-10T09:34:25,053     writing top-level names to /tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info/top_level.txt
2021-07-10T09:34:25,054     writing manifest file '/tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info/SOURCES.txt'
2021-07-10T09:34:25,536     reading manifest file '/tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info/SOURCES.txt'
2021-07-10T09:34:25,538     reading manifest template 'MANIFEST.in'
2021-07-10T09:34:25,594     writing manifest file '/tmp/pip-pip-egg-info-utat2acn/mdtraj.egg-info/SOURCES.txt'
2021-07-10T09:34:25,699   Source in /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac has version 1.5.0, which satisfies requirement mdtraj==1.5.0 from https://files.pythonhosted.org/packages/b2/2c/1cfc1f7879ea82293afca1edd595f3ca39e25f8411627175e88ea6819f83/mdtraj-1.5.0.zip#sha256=e56dcf4b7be97c007692b6c6758f8fc8b84811e666de1c3836631e697dab9394
2021-07-10T09:34:25,700   Removed mdtraj==1.5.0 from https://files.pythonhosted.org/packages/b2/2c/1cfc1f7879ea82293afca1edd595f3ca39e25f8411627175e88ea6819f83/mdtraj-1.5.0.zip#sha256=e56dcf4b7be97c007692b6c6758f8fc8b84811e666de1c3836631e697dab9394 from build tracker '/tmp/pip-req-tracker-mvoifg0p'
2021-07-10T09:34:25,705 Created temporary directory: /tmp/pip-unpack-xr38fvqf
2021-07-10T09:34:25,705 Building wheels for collected packages: mdtraj
2021-07-10T09:34:25,709   Created temporary directory: /tmp/pip-wheel-88021u0q
2021-07-10T09:34:25,710   Building wheel for mdtraj (setup.py): started
2021-07-10T09:34:25,710   Destination directory: /tmp/pip-wheel-88021u0q
2021-07-10T09:34:25,710   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-88021u0q
2021-07-10T09:34:26,579   C compiler:
2021-07-10T09:34:26,586   Using built-in specs.
2021-07-10T09:34:26,587   COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc
2021-07-10T09:34:26,587   COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper
2021-07-10T09:34:26,587   Target: arm-linux-gnueabihf
2021-07-10T09:34:26,587   Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
2021-07-10T09:34:26,587   Thread model: posix
2021-07-10T09:34:26,587   Supported LTO compression algorithms: zlib zstd
2021-07-10T09:34:26,588   gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
2021-07-10T09:34:27,141   Attempting to autodetect OpenMP support... Compiler supports OpenMP
2021-07-10T09:34:27,313   Attempting to autodetect SSE3   support... Did not detect SSE3 support
2021-07-10T09:34:27,483   Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support

2021-07-10T09:34:27,669   running bdist_wheel
2021-07-10T09:34:27,928   running build
2021-07-10T09:34:27,929   running build_py
2021-07-10T09:34:28,069   creating build
2021-07-10T09:34:28,069   creating build/lib.linux-armv7l-3.9
2021-07-10T09:34:28,069   creating build/lib.linux-armv7l-3.9/mdtraj
2021-07-10T09:34:28,071   copying mdtraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-10T09:34:28,072   copying mdtraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-10T09:34:28,075   copying mdtraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-10T09:34:28,078   creating build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,079   copying mdtraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,081   copying mdtraj/utils/validation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,083   copying mdtraj/utils/rotation.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,086   copying mdtraj/utils/six.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,089   copying mdtraj/utils/contextmanagers.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,091   copying mdtraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,093   copying mdtraj/utils/zipped.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,095   copying mdtraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,097   copying mdtraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-10T09:34:28,100   creating build/lib.linux-armv7l-3.9/mdtraj/core
2021-07-10T09:34:28,101   copying mdtraj/core/residue_names.py -> build/lib.linux-armv7l-3.9/mdtraj/core
2021-07-10T09:34:28,103   copying mdtraj/core/topology.py -> build/lib.linux-armv7l-3.9/mdtraj/core
2021-07-10T09:34:28,107   copying mdtraj/core/element.py -> build/lib.linux-armv7l-3.9/mdtraj/core
2021-07-10T09:34:28,110   copying mdtraj/core/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/core
2021-07-10T09:34:28,115   copying mdtraj/core/selection.py -> build/lib.linux-armv7l-3.9/mdtraj/core
2021-07-10T09:34:28,117   copying mdtraj/core/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/core
2021-07-10T09:34:28,120   creating build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-10T09:34:28,120   copying mdtraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-10T09:34:28,122   copying mdtraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-10T09:34:28,125   copying mdtraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-10T09:34:28,127   copying mdtraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-10T09:34:28,129   copying mdtraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-10T09:34:28,132   creating build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,133   copying mdtraj/formats/amberrst.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,136   copying mdtraj/formats/hoomdxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,138   copying mdtraj/formats/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,141   copying mdtraj/formats/arc.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,144   copying mdtraj/formats/mol2.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,147   copying mdtraj/formats/lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,150   copying mdtraj/formats/psf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,152   copying mdtraj/formats/openmmxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,154   copying mdtraj/formats/registry.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,155   copying mdtraj/formats/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,158   copying mdtraj/formats/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,161   copying mdtraj/formats/prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,163   copying mdtraj/formats/xyzfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,166   copying mdtraj/formats/gro.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,168   copying mdtraj/formats/lammpstrj.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,171   copying mdtraj/formats/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:34:28,176   creating build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,177   copying mdtraj/tests/test_crd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,179   copying mdtraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,181   copying mdtraj/tests/test_nmr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,183   copying mdtraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,186   copying mdtraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,189   copying mdtraj/tests/test_arc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,191   copying mdtraj/tests/test_rmsd_memmap.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,193   copying mdtraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,195   copying mdtraj/tests/test_quaternion.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,198   copying mdtraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,200   copying mdtraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,202   copying mdtraj/tests/test_xyz.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,204   copying mdtraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,207   copying mdtraj/tests/test_capi.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,209   copying mdtraj/tests/test_dtr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,212   copying mdtraj/tests/test_docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,214   copying mdtraj/tests/test_lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,216   copying mdtraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,219   copying mdtraj/tests/test_prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,221   copying mdtraj/tests/test_hoomdxml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,223   copying mdtraj/tests/test_selection.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,226   copying mdtraj/tests/test_mol2.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,229   copying mdtraj/tests/test_restart.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,231   copying mdtraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,234   copying mdtraj/tests/test_lammpstrj.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,236   copying mdtraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,239   copying mdtraj/tests/test_gro.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,241   copying mdtraj/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,243   copying mdtraj/tests/test_lprmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,245   copying mdtraj/tests/test_topology.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,247   copying mdtraj/tests/test_psf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,250   copying mdtraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,252   copying mdtraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,255   copying mdtraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,258   copying mdtraj/tests/test_zipped.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,260   copying mdtraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-10T09:34:28,263   creating build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,264   copying mdtraj/geometry/order.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,267   copying mdtraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,270   copying mdtraj/geometry/sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,272   copying mdtraj/geometry/rdf.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,274   copying mdtraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,276   copying mdtraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,279   copying mdtraj/geometry/hbond.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,282   copying mdtraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,284   copying mdtraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,286   copying mdtraj/geometry/thermodynamic_properties.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,289   copying mdtraj/geometry/contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,291   copying mdtraj/geometry/dssp.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,293   copying mdtraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,296   copying mdtraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-10T09:34:28,299   creating build/lib.linux-armv7l-3.9/mdtraj/scripts
2021-07-10T09:34:28,299   copying mdtraj/scripts/mdinspect.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts
2021-07-10T09:34:28,302   copying mdtraj/scripts/mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts
2021-07-10T09:34:28,305   copying mdtraj/scripts/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts
2021-07-10T09:34:28,307   creating build/lib.linux-armv7l-3.9/mdtraj/nmr
2021-07-10T09:34:28,308   copying mdtraj/nmr/scalar_couplings.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr
2021-07-10T09:34:28,311   copying mdtraj/nmr/shift_wrappers.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr
2021-07-10T09:34:28,313   copying mdtraj/nmr/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/nmr
2021-07-10T09:34:28,316   creating build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-10T09:34:28,317   copying mdtraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-10T09:34:28,320   copying mdtraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-10T09:34:28,323   copying mdtraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-10T09:34:28,325   copying mdtraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-10T09:34:28,327   copying mdtraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-10T09:34:28,330   creating build/lib.linux-armv7l-3.9/mdtraj/html
2021-07-10T09:34:28,331   copying mdtraj/html/install.py -> build/lib.linux-armv7l-3.9/mdtraj/html
2021-07-10T09:34:28,333   copying mdtraj/html/imagebutton_widget.py -> build/lib.linux-armv7l-3.9/mdtraj/html
2021-07-10T09:34:28,335   copying mdtraj/html/linked_heatmap.py -> build/lib.linux-armv7l-3.9/mdtraj/html
2021-07-10T09:34:28,337   copying mdtraj/html/trajectory_widget.py -> build/lib.linux-armv7l-3.9/mdtraj/html
2021-07-10T09:34:28,340   copying mdtraj/html/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/html
2021-07-10T09:34:28,343   creating build/lib.linux-armv7l-3.9/mdtraj/utils/external
2021-07-10T09:34:28,344   copying mdtraj/utils/external/pyparsing.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external
2021-07-10T09:34:28,350   copying mdtraj/utils/external/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external
2021-07-10T09:34:28,354   creating build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,355   copying mdtraj/utils/unit/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,359   copying mdtraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,361   copying mdtraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,364   copying mdtraj/utils/unit/prefix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,367   copying mdtraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,369   copying mdtraj/utils/unit/quantity.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,373   copying mdtraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,375   copying mdtraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,378   copying mdtraj/utils/unit/doctests.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,381   copying mdtraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,384   copying mdtraj/utils/unit/constants.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,386   copying mdtraj/utils/unit/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,388   copying mdtraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit
2021-07-10T09:34:28,392   creating build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor
2021-07-10T09:34:28,393   copying mdtraj/utils/external/astor/misc.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor
2021-07-10T09:34:28,395   copying mdtraj/utils/external/astor/treewalk.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor
2021-07-10T09:34:28,398   copying mdtraj/utils/external/astor/codegen.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor
2021-07-10T09:34:28,401   copying mdtraj/utils/external/astor/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/external/astor
2021-07-10T09:34:28,403   creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb
2021-07-10T09:34:28,404   copying mdtraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb
2021-07-10T09:34:28,408   copying mdtraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb
2021-07-10T09:34:28,410   copying mdtraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb
2021-07-10T09:34:28,413   creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests
2021-07-10T09:34:28,414   copying mdtraj/formats/pdb/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests
2021-07-10T09:34:28,416   copying mdtraj/formats/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests
2021-07-10T09:34:28,419   copying mdtraj/formats/pdb/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests
2021-07-10T09:34:28,422   creating build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,422   copying mdtraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,424   copying mdtraj/geometry/tests/test_angles.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,426   copying mdtraj/geometry/tests/test_thermodynamic_properties.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,429   copying mdtraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,431   copying mdtraj/geometry/tests/test_drid.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,433   copying mdtraj/geometry/tests/test_rdf.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,435   copying mdtraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,437   copying mdtraj/geometry/tests/test_dssp.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,439   copying mdtraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,442   copying mdtraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,444   copying mdtraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,447   copying mdtraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,449   copying mdtraj/geometry/tests/test_order.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,451   copying mdtraj/geometry/tests/test_neighbors.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,452   copying mdtraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests
2021-07-10T09:34:28,479   creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,479   copying mdtraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,521   copying mdtraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,525   copying mdtraj/testing/reference/1ncw.pdb.gz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,532   copying mdtraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,534   copying mdtraj/testing/reference/test_hoomdxml.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,576   copying mdtraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,578   copying mdtraj/testing/reference/1vii.pdb.gz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,580   copying mdtraj/testing/reference/freesolve_v0.3.tar.bz2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,591   copying mdtraj/testing/reference/1am7_uncorrected.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,606   copying mdtraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,624   copying mdtraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,626   copying mdtraj/testing/reference/tip3p_300K_1ATM_all-all_rdf.xvg -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,629   copying mdtraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,632   copying mdtraj/testing/reference/test.parm7 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,687   copying mdtraj/testing/reference/tip3p_300K_1ATM_O-O_rdf.xvg -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,689   copying mdtraj/testing/reference/ala_ala_ala.psf -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,692   copying mdtraj/testing/reference/tip3p_300K_1ATM.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,720   copying mdtraj/testing/reference/alanine-dipeptide-explicit.prmtop -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,730   copying mdtraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,750   copying mdtraj/testing/reference/imatinib.mol2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,753   copying mdtraj/testing/reference/no_chains.hoomdxml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,757   copying mdtraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,759   copying mdtraj/testing/reference/custom.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,762   copying mdtraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,768   copying mdtraj/testing/reference/ala_ala_ala.mdcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,771   copying mdtraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,775   copying mdtraj/testing/reference/alanine-dipeptide-explicit.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,779   copying mdtraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,788   copying mdtraj/testing/reference/lysozyme-ligand-tripos.mol2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,790   copying mdtraj/testing/reference/test_good.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:28,875   copying mdtraj/testing/reference/3pqr_memb.psf -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,404   copying mdtraj/testing/reference/no_ions.hoomdxml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,409   copying mdtraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,411   copying mdtraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,414   copying mdtraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,416   copying mdtraj/testing/reference/ala_ala_ala.xpsf -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,419   copying mdtraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,423   copying mdtraj/testing/reference/1vii.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,427   copying mdtraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,429   copying mdtraj/testing/reference/ala_dipeptide.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,437   copying mdtraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,441   copying mdtraj/testing/reference/2lines.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,443   copying mdtraj/testing/reference/3lines.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,446   copying mdtraj/testing/reference/imatinib.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,449   copying mdtraj/testing/reference/alanine.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,451   copying mdtraj/testing/reference/monolayer.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,463   copying mdtraj/testing/reference/frame0.xyz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,484   copying mdtraj/testing/reference/nitrogen.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,503   copying mdtraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,505   copying mdtraj/testing/reference/1line.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,508   copying mdtraj/testing/reference/status-bits.mol2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,510   copying mdtraj/testing/reference/frame0.gro -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,529   copying mdtraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:29,552   copying mdtraj/testing/reference/overflow.crd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,128   copying mdtraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,136   copying mdtraj/testing/reference/smooth.txt -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,140   copying mdtraj/testing/reference/ala_dipeptide.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,146   copying mdtraj/testing/reference/inpcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,155   copying mdtraj/testing/reference/1am7_corrected.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,170   copying mdtraj/testing/reference/ala_ala_ala.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,172   copying mdtraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,183   copying mdtraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,186   copying mdtraj/testing/reference/custom.lammpstrj -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,189   copying mdtraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,191   copying mdtraj/testing/reference/tz2.truncoct.parm7 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,222   copying mdtraj/testing/reference/well-mixed.hoomdxml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,236   copying mdtraj/testing/reference/water_hex.pdb.gz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,280   copying mdtraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,284   copying mdtraj/testing/reference/1am7_protein.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,292   copying mdtraj/testing/reference/ala3_chamber.parm7 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,296   copying mdtraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,306   copying mdtraj/testing/reference/md.mdp -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,308   copying mdtraj/testing/reference/frame0.lammpstrj -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,323   copying mdtraj/testing/reference/3nch.pdb.gz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,337   copying mdtraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,347   copying mdtraj/testing/reference/tip3p_300K_1ATM.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,352   copying mdtraj/testing/reference/4OH9.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,358   copying mdtraj/testing/reference/alanine-dipeptide-explicit.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,366   copying mdtraj/testing/reference/nitrogen.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,388   copying mdtraj/testing/reference/ncinpcrd.rst7 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,393   copying mdtraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,402   copying mdtraj/testing/reference/native2.xml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,404   copying mdtraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,411   copying mdtraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,413   copying mdtraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,417   copying mdtraj/testing/reference/alanine-dipeptide-implicit.prmtop -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,421   copying mdtraj/testing/reference/monolayer.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,459   copying mdtraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,474   copying mdtraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,490   copying mdtraj/testing/reference/native.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,493   copying mdtraj/testing/reference/adp.mol2 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,496   copying mdtraj/testing/reference/test_bad.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,543   copying mdtraj/testing/reference/v_error.gro -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,545   copying mdtraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,551   copying mdtraj/testing/reference/tip3p_300K_1ATM_O-H_rdf.xvg -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,554   copying mdtraj/testing/reference/README.md -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,557   copying mdtraj/testing/reference/frame0.xyz.gz -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-10T09:34:31,561   creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference/ala_dipeptide_trj
2021-07-10T09:34:31,562   copying mdtraj/testing/reference/ala_dipeptide_trj/metadata -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/ala_dipeptide_trj
2021-07-10T09:34:31,565   copying mdtraj/testing/reference/ala_dipeptide_trj/timekeys -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/ala_dipeptide_trj
2021-07-10T09:34:31,567   copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000001 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/ala_dipeptide_trj
2021-07-10T09:34:31,571   copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000002 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/ala_dipeptide_trj
2021-07-10T09:34:31,575   copying mdtraj/testing/reference/ala_dipeptide_trj/clickme.dtr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/ala_dipeptide_trj
2021-07-10T09:34:31,577   copying mdtraj/testing/reference/ala_dipeptide_trj/frame000000000 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/ala_dipeptide_trj
2021-07-10T09:34:31,581   creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference/frame0.dtr
2021-07-10T09:34:31,582   copying mdtraj/testing/reference/frame0.dtr/metadata -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/frame0.dtr
2021-07-10T09:34:31,585   copying mdtraj/testing/reference/frame0.dtr/timekeys -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/frame0.dtr
2021-07-10T09:34:31,588   copying mdtraj/testing/reference/frame0.dtr/frame000000001 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/frame0.dtr
2021-07-10T09:34:31,621   copying mdtraj/testing/reference/frame0.dtr/clickme.dtr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/frame0.dtr
2021-07-10T09:34:31,623   copying mdtraj/testing/reference/frame0.dtr/frame000000000 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference/frame0.dtr
2021-07-10T09:34:31,650   creating build/lib.linux-armv7l-3.9/mdtraj/html/static
2021-07-10T09:34:31,651   copying mdtraj/html/static/widget_trajectory.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static
2021-07-10T09:34:31,654   copying mdtraj/html/static/context.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static
2021-07-10T09:34:31,656   copying mdtraj/html/static/iview.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static
2021-07-10T09:34:31,660   copying mdtraj/html/static/surface.min.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static
2021-07-10T09:34:31,664   copying mdtraj/html/static/filesaver.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static
2021-07-10T09:34:31,667   copying mdtraj/html/static/objexporter.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static
2021-07-10T09:34:31,669   copying mdtraj/html/static/widget_imagebutton.js -> build/lib.linux-armv7l-3.9/mdtraj/html/static
2021-07-10T09:34:31,671   creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data
2021-07-10T09:34:31,672   copying mdtraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data
2021-07-10T09:34:31,676   copying mdtraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data
2021-07-10T09:34:31,696   running build_ext
2021-07-10T09:34:31,699   cythoning mdtraj/formats/xtc/xtc.pyx to mdtraj/formats/xtc/xtc.c
2021-07-10T09:34:32,323   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/formats/xtc/xtc.pyx
2021-07-10T09:34:32,323     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:34,815   cythoning mdtraj/formats/xtc/trr.pyx to mdtraj/formats/xtc/trr.c
2021-07-10T09:34:34,825   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/formats/xtc/trr.pyx
2021-07-10T09:34:34,825     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:37,162   cythoning mdtraj/formats/dcd/dcd.pyx to mdtraj/formats/dcd/dcd.c
2021-07-10T09:34:37,175   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/formats/dcd/dcd.pyx
2021-07-10T09:34:37,175     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:39,527   cythoning mdtraj/formats/binpos/binpos.pyx to mdtraj/formats/binpos/binpos.c
2021-07-10T09:34:39,546   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/formats/binpos/binpos.pyx
2021-07-10T09:34:39,546     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:41,671   cythoning mdtraj/formats/dtr/dtr.pyx to mdtraj/formats/dtr/dtr.cpp
2021-07-10T09:34:41,682   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/formats/dtr/dtr.pyx
2021-07-10T09:34:41,683     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:44,884   cythoning mdtraj/rmsd/_rmsd.pyx to mdtraj/rmsd/_rmsd.c
2021-07-10T09:34:44,902   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/rmsd/_rmsd.pyx
2021-07-10T09:34:44,902     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:48,084   warning: mdtraj/rmsd/_rmsd.pyx:187:62: Use boundscheck(False) for faster access
2021-07-10T09:34:48,085   warning: mdtraj/rmsd/_rmsd.pyx:187:87: Use boundscheck(False) for faster access
2021-07-10T09:34:48,086   warning: mdtraj/rmsd/_rmsd.pyx:187:103: Use boundscheck(False) for faster access
2021-07-10T09:34:48,087   warning: mdtraj/rmsd/_rmsd.pyx:188:21: Use boundscheck(False) for faster access
2021-07-10T09:34:48,249   cythoning mdtraj/rmsd/_lprmsd.pyx to mdtraj/rmsd/_lprmsd.cpp
2021-07-10T09:34:48,258   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/rmsd/_lprmsd.pyx
2021-07-10T09:34:48,259     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:51,472   cythoning mdtraj/geometry/src/_geometry.pyx to mdtraj/geometry/src/_geometry.cpp
2021-07-10T09:34:51,484   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/geometry/src/_geometry.pyx
2021-07-10T09:34:51,484     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:57,262   cythoning mdtraj/geometry/drid.pyx to mdtraj/geometry/drid.c
2021-07-10T09:34:57,275   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/geometry/drid.pyx
2021-07-10T09:34:57,275     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:34:58,760   cythoning mdtraj/geometry/neighbors.pyx to mdtraj/geometry/neighbors.cpp
2021-07-10T09:34:58,770   /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/mdtraj/geometry/neighbors.pyx
2021-07-10T09:34:58,770     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-10T09:35:04,216   building 'mdtraj.formats.xtc' extension
2021-07-10T09:35:04,217   creating build/temp.linux-armv7l-3.9
2021-07-10T09:35:04,217   creating build/temp.linux-armv7l-3.9/mdtraj
2021-07-10T09:35:04,218   creating build/temp.linux-armv7l-3.9/mdtraj/formats
2021-07-10T09:35:04,218   creating build/temp.linux-armv7l-3.9/mdtraj/formats/xtc
2021-07-10T09:35:04,219   creating build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src
2021-07-10T09:35:04,220   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile.o
2021-07-10T09:35:04,400   mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’:
2021-07-10T09:35:04,401   mdtraj/formats/xtc/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,401     495 |     while (size >= num && num_of_bits < 32)
2021-07-10T09:35:04,401         |                 ^~
2021-07-10T09:35:04,401   mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’:
2021-07-10T09:35:04,401   mdtraj/formats/xtc/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,401     541 |     while (bytes[num_of_bytes] >= num)
2021-07-10T09:35:04,402         |                                ^~
2021-07-10T09:35:04,402   mdtraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’:
2021-07-10T09:35:04,402   mdtraj/formats/xtc/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,403     650 |     if (num_of_bits >= num_of_bytes * 8)
2021-07-10T09:35:04,403         |                     ^~
2021-07-10T09:35:04,403   mdtraj/formats/xtc/src/xdrfile.c:652:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,403     652 |   for (i = 0; i < num_of_bytes; i++)
2021-07-10T09:35:04,403         |                 ^
2021-07-10T09:35:04,403   mdtraj/formats/xtc/src/xdrfile.c:660:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,404     660 |   for (i = 0; i < num_of_bytes-1; i++)
2021-07-10T09:35:04,404         |                 ^
2021-07-10T09:35:04,404   mdtraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’:
2021-07-10T09:35:04,404   mdtraj/formats/xtc/src/xdrfile.c:700:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,404     700 |   if (lastbits < num_of_bits)
2021-07-10T09:35:04,404         |                ^
2021-07-10T09:35:04,406   mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
2021-07-10T09:35:04,406   mdtraj/formats/xtc/src/xdrfile.c:815:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,406     815 |  if(size3>xfp->buf1size)
2021-07-10T09:35:04,406         |          ^
2021-07-10T09:35:04,408   mdtraj/formats/xtc/src/xdrfile.c:869:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,408     869 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:04,408         |                   ^
2021-07-10T09:35:04,408   mdtraj/formats/xtc/src/xdrfile.c:869:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-10T09:35:04,409     869 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:04,409         |                                     ^~~
2021-07-10T09:35:04,410   mdtraj/formats/xtc/src/xdrfile.c:928:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,410     928 |   if ((lfp-ptrstart)+run > size3)
2021-07-10T09:35:04,410         |                          ^
2021-07-10T09:35:04,412   mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:04,412     788 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-10T09:35:04,412         |                         ^~~~~~
2021-07-10T09:35:04,412   mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:04,412     785 |  int smallidx, minidx, maxidx;
2021-07-10T09:35:04,412         |                ^~~~~~
2021-07-10T09:35:04,413   mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
2021-07-10T09:35:04,413   mdtraj/formats/xtc/src/xdrfile.c:1027:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,413    1027 |  if(size3>xfp->buf1size)
2021-07-10T09:35:04,414         |          ^
2021-07-10T09:35:04,418   mdtraj/formats/xtc/src/xdrfile.c:1150:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,419    1150 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
2021-07-10T09:35:04,419         |                  ^
2021-07-10T09:35:04,419   mdtraj/formats/xtc/src/xdrfile.c:1156:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,419    1156 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:04,419         |                   ^
2021-07-10T09:35:04,420   mdtraj/formats/xtc/src/xdrfile.c:1156:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-10T09:35:04,420    1156 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:04,420         |                                     ^~~
2021-07-10T09:35:04,423   mdtraj/formats/xtc/src/xdrfile.c:1288:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,423    1288 |  if(tmp==(unsigned int)buf2[0])
2021-07-10T09:35:04,423         |        ^~
2021-07-10T09:35:04,424   mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:04,424    1016 |  int errval=1;
2021-07-10T09:35:04,424         |      ^~~~~~
2021-07-10T09:35:04,425   mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
2021-07-10T09:35:04,426   mdtraj/formats/xtc/src/xdrfile.c:1328:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,426    1328 |  if(size3>xfp->buf1size)
2021-07-10T09:35:04,426         |          ^
2021-07-10T09:35:04,428   mdtraj/formats/xtc/src/xdrfile.c:1383:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,428    1383 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:04,428         |                   ^
2021-07-10T09:35:04,429   mdtraj/formats/xtc/src/xdrfile.c:1383:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-10T09:35:04,429    1383 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:04,429         |                                     ^~~
2021-07-10T09:35:04,432   mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:04,432    1305 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-10T09:35:04,432         |                         ^~~~~~
2021-07-10T09:35:04,432   mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:04,433    1302 |  int smallidx, minidx, maxidx;
2021-07-10T09:35:04,433         |                ^~~~~~
2021-07-10T09:35:04,433   mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
2021-07-10T09:35:04,434   mdtraj/formats/xtc/src/xdrfile.c:1519:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,434    1519 |  if(size3>xfp->buf1size) {
2021-07-10T09:35:04,434         |          ^
2021-07-10T09:35:04,442   mdtraj/formats/xtc/src/xdrfile.c:1634:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,442    1634 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
2021-07-10T09:35:04,442         |                  ^
2021-07-10T09:35:04,443   mdtraj/formats/xtc/src/xdrfile.c:1639:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:04,443    1639 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:04,443         |                   ^
2021-07-10T09:35:04,444   mdtraj/formats/xtc/src/xdrfile.c:1639:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-10T09:35:04,444    1639 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:04,444         |                                     ^~~
2021-07-10T09:35:04,448   mdtraj/formats/xtc/src/xdrfile.c:1749:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:04,448    1749 |  if(tmp==(unsigned int)buf2[0])
2021-07-10T09:35:04,448         |        ^~
2021-07-10T09:35:04,449   mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:04,449    1509 |  int errval=1;
2021-07-10T09:35:04,449         |      ^~~~~~
2021-07-10T09:35:06,592   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o
2021-07-10T09:35:06,683   mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’:
2021-07-10T09:35:06,683   mdtraj/formats/xtc/src/xdrfile_xtc.c:66:8: warning: unused variable ‘j’ [-Wunused-variable]
2021-07-10T09:35:06,683      66 |  int i,j,result;
2021-07-10T09:35:06,683         |        ^
2021-07-10T09:35:06,684   mdtraj/formats/xtc/src/xdrfile_xtc.c:66:6: warning: unused variable ‘i’ [-Wunused-variable]
2021-07-10T09:35:06,684      66 |  int i,j,result;
2021-07-10T09:35:06,684         |      ^
2021-07-10T09:35:06,685   mdtraj/formats/xtc/src/xdrfile_xtc.c: In function ‘read_xtc_nframes’:
2021-07-10T09:35:06,685   mdtraj/formats/xtc/src/xdrfile_xtc.c:119:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
2021-07-10T09:35:06,685     119 |     if (NULL == xd)
2021-07-10T09:35:06,685         |     ^~
2021-07-10T09:35:06,686   mdtraj/formats/xtc/src/xdrfile_xtc.c:122:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
2021-07-10T09:35:06,686     122 |  do {
2021-07-10T09:35:06,686         |  ^~
2021-07-10T09:35:06,831   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/xtc.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/xtc.o
2021-07-10T09:35:07,238   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-10T09:35:07,239                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-10T09:35:07,239                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-10T09:35:07,239                    from mdtraj/formats/xtc/xtc.c:612:
2021-07-10T09:35:07,239   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-10T09:35:07,239      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-10T09:35:07,239         |  ^~~~~~~
2021-07-10T09:35:07,579   mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_26__len__’:
2021-07-10T09:35:07,583   mdtraj/formats/xtc/xtc.c:9464:40: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
2021-07-10T09:35:07,584    9464 |   __pyx_t_3 = ((__pyx_v_self->n_frames == -1L) != 0);
2021-07-10T09:35:07,584         |                                        ^~
2021-07-10T09:35:11,999   mdtraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_16_write’:
2021-07-10T09:35:11,999   mdtraj/formats/xtc/xtc.c:526:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-10T09:35:11,999     526 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-10T09:35:11,999         |                                        ^~~~~~~~~~~~~~~
2021-07-10T09:35:12,004   mdtraj/formats/xtc/xtc.c:8236:7: note: ‘__pyx_v_status’ was declared here
2021-07-10T09:35:12,004    8236 |   int __pyx_v_status;
2021-07-10T09:35:12,004         |       ^~~~~~~~~~~~~~
2021-07-10T09:35:22,620   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/xtc.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so
2021-07-10T09:35:22,796   building 'mdtraj.formats.trr' extension
2021-07-10T09:35:22,797   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile.o
2021-07-10T09:35:22,955   mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’:
2021-07-10T09:35:22,955   mdtraj/formats/xtc/src/xdrfile.c:495:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,956     495 |     while (size >= num && num_of_bits < 32)
2021-07-10T09:35:22,956         |                 ^~
2021-07-10T09:35:22,956   mdtraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’:
2021-07-10T09:35:22,956   mdtraj/formats/xtc/src/xdrfile.c:541:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,956     541 |     while (bytes[num_of_bytes] >= num)
2021-07-10T09:35:22,956         |                                ^~
2021-07-10T09:35:22,957   mdtraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’:
2021-07-10T09:35:22,957   mdtraj/formats/xtc/src/xdrfile.c:650:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,957     650 |     if (num_of_bits >= num_of_bytes * 8)
2021-07-10T09:35:22,957         |                     ^~
2021-07-10T09:35:22,958   mdtraj/formats/xtc/src/xdrfile.c:652:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,958     652 |   for (i = 0; i < num_of_bytes; i++)
2021-07-10T09:35:22,958         |                 ^
2021-07-10T09:35:22,958   mdtraj/formats/xtc/src/xdrfile.c:660:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,958     660 |   for (i = 0; i < num_of_bytes-1; i++)
2021-07-10T09:35:22,958         |                 ^
2021-07-10T09:35:22,958   mdtraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’:
2021-07-10T09:35:22,959   mdtraj/formats/xtc/src/xdrfile.c:700:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,959     700 |   if (lastbits < num_of_bits)
2021-07-10T09:35:22,959         |                ^
2021-07-10T09:35:22,960   mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
2021-07-10T09:35:22,960   mdtraj/formats/xtc/src/xdrfile.c:815:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,960     815 |  if(size3>xfp->buf1size)
2021-07-10T09:35:22,961         |          ^
2021-07-10T09:35:22,962   mdtraj/formats/xtc/src/xdrfile.c:869:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,962     869 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:22,962         |                   ^
2021-07-10T09:35:22,962   mdtraj/formats/xtc/src/xdrfile.c:869:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-10T09:35:22,962     869 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:22,962         |                                     ^~~
2021-07-10T09:35:22,963   mdtraj/formats/xtc/src/xdrfile.c:928:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,964     928 |   if ((lfp-ptrstart)+run > size3)
2021-07-10T09:35:22,964         |                          ^
2021-07-10T09:35:22,965   mdtraj/formats/xtc/src/xdrfile.c:788:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:22,965     788 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-10T09:35:22,965         |                         ^~~~~~
2021-07-10T09:35:22,965   mdtraj/formats/xtc/src/xdrfile.c:785:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:22,965     785 |  int smallidx, minidx, maxidx;
2021-07-10T09:35:22,965         |                ^~~~~~
2021-07-10T09:35:22,966   mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
2021-07-10T09:35:22,966   mdtraj/formats/xtc/src/xdrfile.c:1027:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,966    1027 |  if(size3>xfp->buf1size)
2021-07-10T09:35:22,966         |          ^
2021-07-10T09:35:22,971   mdtraj/formats/xtc/src/xdrfile.c:1150:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,971    1150 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
2021-07-10T09:35:22,971         |                  ^
2021-07-10T09:35:22,971   mdtraj/formats/xtc/src/xdrfile.c:1156:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,971    1156 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:22,971         |                   ^
2021-07-10T09:35:22,972   mdtraj/formats/xtc/src/xdrfile.c:1156:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-10T09:35:22,972    1156 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:22,972         |                                     ^~~
2021-07-10T09:35:22,975   mdtraj/formats/xtc/src/xdrfile.c:1288:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,975    1288 |  if(tmp==(unsigned int)buf2[0])
2021-07-10T09:35:22,975         |        ^~
2021-07-10T09:35:22,975   mdtraj/formats/xtc/src/xdrfile.c:1016:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:22,975    1016 |  int errval=1;
2021-07-10T09:35:22,975         |      ^~~~~~
2021-07-10T09:35:22,976   mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
2021-07-10T09:35:22,977   mdtraj/formats/xtc/src/xdrfile.c:1328:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,977    1328 |  if(size3>xfp->buf1size)
2021-07-10T09:35:22,977         |          ^
2021-07-10T09:35:22,979   mdtraj/formats/xtc/src/xdrfile.c:1383:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,979    1383 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:22,979         |                   ^
2021-07-10T09:35:22,979   mdtraj/formats/xtc/src/xdrfile.c:1383:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-10T09:35:22,979    1383 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:22,979         |                                     ^~~
2021-07-10T09:35:22,982   mdtraj/formats/xtc/src/xdrfile.c:1305:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:22,982    1305 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-10T09:35:22,982         |                         ^~~~~~
2021-07-10T09:35:22,982   mdtraj/formats/xtc/src/xdrfile.c:1302:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:22,983    1302 |  int smallidx, minidx, maxidx;
2021-07-10T09:35:22,983         |                ^~~~~~
2021-07-10T09:35:22,983   mdtraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
2021-07-10T09:35:22,984   mdtraj/formats/xtc/src/xdrfile.c:1519:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,984    1519 |  if(size3>xfp->buf1size) {
2021-07-10T09:35:22,984         |          ^
2021-07-10T09:35:22,990   mdtraj/formats/xtc/src/xdrfile.c:1634:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,990    1634 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
2021-07-10T09:35:22,990         |                  ^
2021-07-10T09:35:22,991   mdtraj/formats/xtc/src/xdrfile.c:1639:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:22,991    1639 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:22,991         |                   ^
2021-07-10T09:35:22,992   mdtraj/formats/xtc/src/xdrfile.c:1639:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-10T09:35:22,992    1639 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-10T09:35:22,992         |                                     ^~~
2021-07-10T09:35:22,995   mdtraj/formats/xtc/src/xdrfile.c:1749:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:22,995    1749 |  if(tmp==(unsigned int)buf2[0])
2021-07-10T09:35:22,995         |        ^~
2021-07-10T09:35:22,996   mdtraj/formats/xtc/src/xdrfile.c:1509:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-10T09:35:22,996    1509 |  int errval=1;
2021-07-10T09:35:22,996         |      ^~~~~~
2021-07-10T09:35:25,137   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o
2021-07-10T09:35:25,244   mdtraj/formats/xtc/src/xdrfile_trr.c: In function ‘do_trnheader’:
2021-07-10T09:35:25,244   mdtraj/formats/xtc/src/xdrfile_trr.c:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-10T09:35:25,245     111 |         if (slen != strlen(version)+1)
2021-07-10T09:35:25,245         |                  ^~
2021-07-10T09:35:25,245   mdtraj/formats/xtc/src/xdrfile_trr.c:121:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-10T09:35:25,245     121 |         if (xdrfile_write_string(version,xd) != (strlen(version)+1) )
2021-07-10T09:35:25,245         |                                              ^~
2021-07-10T09:35:25,252   mdtraj/formats/xtc/src/xdrfile_trr.c: In function ‘read_trr_nframes’:
2021-07-10T09:35:25,252   mdtraj/formats/xtc/src/xdrfile_trr.c:504:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
2021-07-10T09:35:25,252     504 |     if (NULL == xd)
2021-07-10T09:35:25,252         |     ^~
2021-07-10T09:35:25,252   mdtraj/formats/xtc/src/xdrfile_trr.c:507:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
2021-07-10T09:35:25,253     507 |  do {
2021-07-10T09:35:25,253         |  ^~
2021-07-10T09:35:25,833   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/xtc/trr.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/trr.o
2021-07-10T09:35:26,220   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-10T09:35:26,220                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-10T09:35:26,220                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-10T09:35:26,221                    from mdtraj/formats/xtc/trr.c:612:
2021-07-10T09:35:26,221   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-10T09:35:26,221      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-10T09:35:26,221         |  ^~~~~~~
2021-07-10T09:35:26,548   mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_26__len__’:
2021-07-10T09:35:26,553   mdtraj/formats/xtc/trr.c:9440:40: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
2021-07-10T09:35:26,553    9440 |   __pyx_t_3 = ((__pyx_v_self->n_frames == -1L) != 0);
2021-07-10T09:35:26,553         |                                        ^~
2021-07-10T09:35:30,838   mdtraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_16_write’:
2021-07-10T09:35:30,839   mdtraj/formats/xtc/trr.c:526:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-10T09:35:30,839     526 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-10T09:35:30,839         |                                        ^~~~~~~~~~~~~~~
2021-07-10T09:35:30,843   mdtraj/formats/xtc/trr.c:8214:7: note: ‘__pyx_v_status’ was declared here
2021-07-10T09:35:30,843    8214 |   int __pyx_v_status;
2021-07-10T09:35:30,844         |       ^~~~~~~~~~~~~~
2021-07-10T09:35:41,789   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-3.9/mdtraj/formats/xtc/trr.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so
2021-07-10T09:35:41,969   building 'mdtraj.formats.dcd' extension
2021-07-10T09:35:41,970   creating build/temp.linux-armv7l-3.9/mdtraj/formats/dcd
2021-07-10T09:35:41,971   creating build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/src
2021-07-10T09:35:41,972   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/dcd.o
2021-07-10T09:35:42,377   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-10T09:35:42,378                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-10T09:35:42,378                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-10T09:35:42,378                    from mdtraj/formats/dcd/dcd.c:612:
2021-07-10T09:35:42,378   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-10T09:35:42,378      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-10T09:35:42,378         |  ^~~~~~~
2021-07-10T09:35:43,129   In file included from mdtraj/formats/dcd/include/dcdplugin.h:1,
2021-07-10T09:35:43,129                    from mdtraj/formats/dcd/dcd.c:621:
2021-07-10T09:35:43,129   mdtraj/formats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
2021-07-10T09:35:43,130     474 | static int fio_write_str(fio_fd fd, const char *str) {
2021-07-10T09:35:43,130         |            ^~~~~~~~~~~~~
2021-07-10T09:35:43,130   mdtraj/formats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
2021-07-10T09:35:43,130     470 | static int fio_read_int32(fio_fd fd, int *i) {
2021-07-10T09:35:43,130         |            ^~~~~~~~~~~~~~
2021-07-10T09:35:43,130   mdtraj/formats/dcd/include/fastio.h:466:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function]
2021-07-10T09:35:43,131     466 | static int fio_write_int32(fio_fd fd, int i) {
2021-07-10T09:35:43,131         |            ^~~~~~~~~~~~~~~
2021-07-10T09:35:43,131   mdtraj/formats/dcd/include/fastio.h:457:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function]
2021-07-10T09:35:43,131     457 | static fio_size_t fio_ftell(fio_fd fd) {
2021-07-10T09:35:43,131         |                   ^~~~~~~~~
2021-07-10T09:35:43,131   mdtraj/formats/dcd/include/fastio.h:450:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function]
2021-07-10T09:35:43,131     450 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {
2021-07-10T09:35:43,131         |                   ^~~~~~~~~
2021-07-10T09:35:43,132   mdtraj/formats/dcd/include/fastio.h:415:19: warning: ‘fio_readv’ defined but not used [-Wunused-function]
2021-07-10T09:35:43,132     415 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {
2021-07-10T09:35:43,132         |                   ^~~~~~~~~
2021-07-10T09:35:43,132   mdtraj/formats/dcd/include/fastio.h:394:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function]
2021-07-10T09:35:43,132     394 | static int fio_fclose(fio_fd fd) {
2021-07-10T09:35:43,132         |            ^~~~~~~~~~
2021-07-10T09:35:43,132   mdtraj/formats/dcd/include/fastio.h:366:12: warning: ‘fio_open’ defined but not used [-Wunused-function]
2021-07-10T09:35:43,132     366 | static int fio_open(const char *filename, int mode, fio_fd *fd) {
2021-07-10T09:35:43,132         |            ^~~~~~~~
2021-07-10T09:35:49,629   mdtraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_20read’:
2021-07-10T09:35:49,629   mdtraj/formats/dcd/dcd.c:526:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-10T09:35:49,629     526 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-10T09:35:49,630         |                                        ^~~~~~~~~~~~~~~
2021-07-10T09:35:49,632   mdtraj/formats/dcd/dcd.c:5241:7: note: ‘__pyx_v_i’ was declared here
2021-07-10T09:35:49,632    5241 |   int __pyx_v_i;
2021-07-10T09:35:49,632         |       ^~~~~~~~~
2021-07-10T09:35:52,694   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/src/dcdplugin.o
2021-07-10T09:35:52,937   mdtraj/formats/dcd/src/dcdplugin.c: In function ‘read_dcdheader’:
2021-07-10T09:35:52,938   mdtraj/formats/dcd/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:52,938     129 |   } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
2021-07-10T09:35:52,938         |                                                         ^~
2021-07-10T09:35:52,939   mdtraj/formats/dcd/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:52,939     146 |       if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
2021-07-10T09:35:52,939         |                                                      ^~
2021-07-10T09:35:52,939   mdtraj/formats/dcd/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:52,939     164 |     if (input_integer[0] != dcdcordmagic) {
2021-07-10T09:35:52,939         |                          ^~
2021-07-10T09:35:52,942   mdtraj/formats/dcd/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:52,942     341 |     if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
2021-07-10T09:35:52,943         |                                             ^~
2021-07-10T09:35:52,943   mdtraj/formats/dcd/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-10T09:35:52,943     358 |     if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
2021-07-10T09:35:52,943         |                                             ^~
2021-07-10T09:35:52,947   mdtraj/formats/dcd/src/dcdplugin.c: In function ‘read_dcdstep’:
2021-07-10T09:35:52,947   mdtraj/formats/dcd/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:52,947     540 |         if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
2021-07-10T09:35:52,947         |                       ^~
2021-07-10T09:35:52,947   mdtraj/formats/dcd/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-10T09:35:52,948     544 |           if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT;
2021-07-10T09:35:52,948         |                                           ^~
2021-07-10T09:35:52,972   In file included from mdtraj/formats/dcd/src/dcdplugin.c:55:
2021-07-10T09:35:52,972   At top level:
2021-07-10T09:35:52,973   mdtraj/formats/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]
2021-07-10T09:35:52,973      96 | static void swap2_aligned(void *v, long ndata) {
2021-07-10T09:35:52,973         |             ^~~~~~~~~~~~~
2021-07-10T09:35:52,973   mdtraj/formats/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]
2021-07-10T09:35:52,973      32 | static void swap2_unaligned(void *v, long ndata) {
2021-07-10T09:35:52,973         |             ^~~~~~~~~~~~~~~
2021-07-10T09:35:52,973   In file included from mdtraj/formats/dcd/src/dcdplugin.c:46:
2021-07-10T09:35:52,974   mdtraj/formats/dcd/include/fastio.h:474:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
2021-07-10T09:35:52,974     474 | static int fio_write_str(fio_fd fd, const char *str) {
2021-07-10T09:35:52,974         |            ^~~~~~~~~~~~~
2021-07-10T09:35:52,974   mdtraj/formats/dcd/include/fastio.h:470:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
2021-07-10T09:35:52,974     470 | static int fio_read_int32(fio_fd fd, int *i) {
2021-07-10T09:35:52,974         |            ^~~~~~~~~~~~~~
2021-07-10T09:35:54,129   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/dcd.o build/temp.linux-armv7l-3.9/mdtraj/formats/dcd/src/dcdplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so
2021-07-10T09:35:54,296   building 'mdtraj.formats.binpos' extension
2021-07-10T09:35:54,297   creating build/temp.linux-armv7l-3.9/mdtraj/formats/binpos
2021-07-10T09:35:54,298   creating build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/src
2021-07-10T09:35:54,299   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/binpos.o
2021-07-10T09:35:54,927   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-10T09:35:54,928                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-10T09:35:54,928                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-10T09:35:54,928                    from mdtraj/formats/binpos/binpos.c:612:
2021-07-10T09:35:54,928   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-10T09:35:54,928      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-10T09:35:54,928         |  ^~~~~~~
2021-07-10T09:36:02,397   mdtraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_9_read’:
2021-07-10T09:36:02,399   mdtraj/formats/binpos/binpos.c:5111:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-10T09:36:02,400    5111 |   if (__pyx_t_2) {
2021-07-10T09:36:02,400         |      ^
2021-07-10T09:36:02,402   mdtraj/formats/binpos/binpos.c:4591:7: note: ‘__pyx_v_status’ was declared here
2021-07-10T09:36:02,402    4591 |   int __pyx_v_status;
2021-07-10T09:36:02,402         |       ^~~~~~~~~~~~~~
2021-07-10T09:36:02,402   mdtraj/formats/binpos/binpos.c:526:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-10T09:36:02,403     526 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-10T09:36:02,403         |                                        ^~~~~~~~~~~~~~~
2021-07-10T09:36:02,405   mdtraj/formats/binpos/binpos.c:4588:7: note: ‘__pyx_v_i’ was declared here
2021-07-10T09:36:02,405    4588 |   int __pyx_v_i;
2021-07-10T09:36:02,405         |       ^~~~~~~~~
2021-07-10T09:36:03,850   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/src/binposplugin.o
2021-07-10T09:36:03,989   mdtraj/formats/binpos/src/binposplugin.c: In function ‘tell_timestep’:
2021-07-10T09:36:03,989   mdtraj/formats/binpos/src/binposplugin.c:128:9: warning: unused variable ‘i’ [-Wunused-variable]
2021-07-10T09:36:03,989     128 |     int i, numatoms, frame;
2021-07-10T09:36:03,989         |         ^
2021-07-10T09:36:04,219   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/binpos.o build/temp.linux-armv7l-3.9/mdtraj/formats/binpos/src/binposplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so
2021-07-10T09:36:04,377   building 'mdtraj.formats.dtr' extension
2021-07-10T09:36:04,378   creating build/temp.linux-armv7l-3.9/mdtraj/formats/dtr
2021-07-10T09:36:04,379   creating build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/src
2021-07-10T09:36:04,380   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/dtr.cpp -o build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/dtr.o
2021-07-10T09:36:04,703   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-10T09:36:04,704                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-10T09:36:04,704                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-10T09:36:04,704                    from mdtraj/formats/dtr/dtr.cpp:626:
2021-07-10T09:36:04,704   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-10T09:36:04,704      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-10T09:36:04,704         |  ^~~~~~~
2021-07-10T09:36:06,074   mdtraj/formats/dtr/dtr.cpp: In function ‘PyObject* __pyx_pf_6mdtraj_7formats_3dtr_17DTRTrajectoryFile_6get_times(__pyx_obj_6mdtraj_7formats_3dtr_DTRTrajectoryFile*)’:
2021-07-10T09:36:06,074   mdtraj/formats/dtr/dtr.cpp:4001:31: warning: comparison of integer expressions of different signedness: ‘molfile_ssize_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-10T09:36:06,075    4001 |   __pyx_t_9 = ((__pyx_v_count != __pyx_v_self->n_frames) != 0);
2021-07-10T09:36:06,075         |                 ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:17,011   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/formats/dtr/src/dtrplugin.cxx -o build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/src/dtrplugin.o
2021-07-10T09:36:18,802   mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const string&)’:
2021-07-10T09:36:18,802   mdtraj/formats/dtr/src/dtrplugin.cxx:486:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
2021-07-10T09:36:18,802     486 |             fprintf(stderr, "non-constant framesize at frame %ld\n", i);
2021-07-10T09:36:18,802         |                                                              ~~^     ~
2021-07-10T09:36:18,802         |                                                                |     |
2021-07-10T09:36:18,803         |                                                                |     size_t {aka unsigned int}
2021-07-10T09:36:18,803         |                                                                long int
2021-07-10T09:36:18,803         |                                                              %d
2021-07-10T09:36:18,803   mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=]
2021-07-10T09:36:18,803     487 |             printf("size %d framesize %d\n\n",
2021-07-10T09:36:18,803         |                          ~^
2021-07-10T09:36:18,804         |                           |
2021-07-10T09:36:18,804         |                           int
2021-07-10T09:36:18,804         |                          %lld
2021-07-10T09:36:18,804     488 |                     keys[i].size(), m_framesize);
2021-07-10T09:36:18,804         |                     ~~~~~~~~~~~~~~
2021-07-10T09:36:18,804         |                                 |
2021-07-10T09:36:18,804         |                                 uint64_t {aka long long unsigned int}
2021-07-10T09:36:18,804   mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=]
2021-07-10T09:36:18,805     487 |             printf("size %d framesize %d\n\n",
2021-07-10T09:36:18,805         |                                       ~^
2021-07-10T09:36:18,805         |                                        |
2021-07-10T09:36:18,805         |                                        int
2021-07-10T09:36:18,805         |                                       %lld
2021-07-10T09:36:18,805     488 |                     keys[i].size(), m_framesize);
2021-07-10T09:36:18,805         |                                     ~~~~~~~~~~~
2021-07-10T09:36:18,806         |                                     |
2021-07-10T09:36:18,806         |                                     uint64_t {aka long long unsigned int}
2021-07-10T09:36:18,806   mdtraj/formats/dtr/src/dtrplugin.cxx:494:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
2021-07-10T09:36:18,806     494 |                     "non-constant time interval at frame %ld\n", i);
2021-07-10T09:36:18,806         |                                                          ~~^     ~
2021-07-10T09:36:18,806         |                                                            |     |
2021-07-10T09:36:18,806         |                                                            |     size_t {aka unsigned int}
2021-07-10T09:36:18,807         |                                                            long int
2021-07-10T09:36:18,807         |                                                          %d
2021-07-10T09:36:18,807   mdtraj/formats/dtr/src/dtrplugin.cxx:499:60: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
2021-07-10T09:36:18,807     499 |             fprintf(stderr, "unexpected offset for frame %ld\n", i);
2021-07-10T09:36:18,807         |                                                          ~~^     ~
2021-07-10T09:36:18,807         |                                                            |     |
2021-07-10T09:36:18,808         |                                                            |     size_t {aka unsigned int}
2021-07-10T09:36:18,808         |                                                            long int
2021-07-10T09:36:18,808         |                                                          %d
2021-07-10T09:36:18,886   mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void* read_file(int, off_t, size_t&)’:
2021-07-10T09:36:18,886   mdtraj/formats/dtr/src/dtrplugin.cxx:902:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-10T09:36:18,887     902 |   if (rc==-1) {
2021-07-10T09:36:18,887         |       ~~^~~~
2021-07-10T09:36:18,932   mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’:
2021-07-10T09:36:18,932   mdtraj/formats/dtr/src/dtrplugin.cxx:1301:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=]
2021-07-10T09:36:18,932    1301 |     fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n",
2021-07-10T09:36:18,933         |                                                                   ~~^
2021-07-10T09:36:18,933         |                                                                     |
2021-07-10T09:36:18,933         |                                                                     long int
2021-07-10T09:36:18,933         |                                                                   %lld
2021-07-10T09:36:18,933    1302 |         3*natoms, pos.count);
2021-07-10T09:36:18,933         |                   ~~~~~~~~~
2021-07-10T09:36:18,933         |                       |
2021-07-10T09:36:18,933         |                       uint64_t {aka long long unsigned int}
2021-07-10T09:36:18,934   mdtraj/formats/dtr/src/dtrplugin.cxx:1310:71: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=]
2021-07-10T09:36:18,934    1310 |       fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n",
2021-07-10T09:36:18,934         |                                                                     ~~^
2021-07-10T09:36:18,934         |                                                                       |
2021-07-10T09:36:18,934         |                                                                       long int
2021-07-10T09:36:18,934         |                                                                     %lld
2021-07-10T09:36:18,935    1311 |           3*natoms, vel.count);
2021-07-10T09:36:18,935         |                     ~~~~~~~~~
2021-07-10T09:36:18,935         |                         |
2021-07-10T09:36:18,935         |                         uint64_t {aka long long unsigned int}
2021-07-10T09:36:18,958   mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)’:
2021-07-10T09:36:18,958   mdtraj/formats/dtr/src/dtrplugin.cxx:1572:45: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=]
2021-07-10T09:36:18,958    1572 |       fprintf(stderr, "VELOCITY field has %ld values; expected %d\n",
2021-07-10T09:36:18,958         |                                           ~~^
2021-07-10T09:36:18,958         |                                             |
2021-07-10T09:36:18,958         |                                             long int
2021-07-10T09:36:18,959         |                                           %lld
2021-07-10T09:36:18,959    1573 |           velblob.count, 3*natoms);
2021-07-10T09:36:18,959         |           ~~~~~~~~~~~~~
2021-07-10T09:36:18,959         |                   |
2021-07-10T09:36:18,959         |                   uint64_t {aka long long unsigned int}
2021-07-10T09:36:19,859   In file included from mdtraj/formats/dtr/src/dtrplugin.cxx:66:
2021-07-10T09:36:19,859   mdtraj/formats/dtr/include/endianswap.h: At global scope:
2021-07-10T09:36:19,859   mdtraj/formats/dtr/include/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function]
2021-07-10T09:36:19,860     124 | static void swap8_aligned(void *v, long ndata) {
2021-07-10T09:36:19,860         |             ^~~~~~~~~~~~~
2021-07-10T09:36:19,860   mdtraj/formats/dtr/include/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function]
2021-07-10T09:36:19,860     110 | static void swap4_aligned(void *v, long ndata) {
2021-07-10T09:36:19,860         |             ^~~~~~~~~~~~~
2021-07-10T09:36:19,860   mdtraj/formats/dtr/include/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function]
2021-07-10T09:36:19,860      96 | static void swap2_aligned(void *v, long ndata) {
2021-07-10T09:36:19,861         |             ^~~~~~~~~~~~~
2021-07-10T09:36:19,861   mdtraj/formats/dtr/include/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function]
2021-07-10T09:36:19,861      32 | static void swap2_unaligned(void *v, long ndata) {
2021-07-10T09:36:19,861         |             ^~~~~~~~~~~~~~~
2021-07-10T09:36:19,861   In file included from mdtraj/formats/dtr/src/dtrplugin.cxx:65:
2021-07-10T09:36:19,861   mdtraj/formats/dtr/include/vmddir.h:132:12: warning: ‘int vmd_file_is_executable(const char*)’ defined but not used [-Wunused-function]
2021-07-10T09:36:19,862     132 | static int vmd_file_is_executable(const char * filename) {
2021-07-10T09:36:19,862         |            ^~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:19,992   mdtraj/formats/dtr/src/dtrplugin.cxx: In constructor ‘{anonymous}::DDException::DDException(const string&, int)’:
2021-07-10T09:36:19,993   mdtraj/formats/dtr/src/dtrplugin.cxx:680:43: warning: ‘*<unknown>.{anonymous}::DDException::eno’ is used uninitialized in this function [-Wuninitialized]
2021-07-10T09:36:19,993     680 |       : std::runtime_error(text + strerror(eno)), eno(_eno){}
2021-07-10T09:36:19,993         |                                   ~~~~~~~~^~~~~
2021-07-10T09:36:22,247   In file included from /usr/include/c++/10/map:60,
2021-07-10T09:36:22,247                    from mdtraj/formats/dtr/src/dtrplugin.cxx:53:
2021-07-10T09:36:22,248   /usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, {anonymous}::Blob>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, {anonymous}::Blob> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, {anonymous}::Blob> >]’:
2021-07-10T09:36:22,248   /usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, {anonymous}::Blob>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, {anonymous}::Blob> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, {anonymous}::Blob> > >::const_iterator’ changed in GCC 7.1
2021-07-10T09:36:22,248    2193 |     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
2021-07-10T09:36:22,248         |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:23,131   mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘void DDmkdir(const string&, mode_t, int, int)’:
2021-07-10T09:36:23,132   mdtraj/formats/dtr/src/dtrplugin.cxx:706:16: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
2021-07-10T09:36:23,132     706 |  sprintf(sub, "%03x/", i);
2021-07-10T09:36:23,132         |                ^~~~
2021-07-10T09:36:23,132   mdtraj/formats/dtr/src/dtrplugin.cxx:706:15: note: directive argument in the range [0, 2147483646]
2021-07-10T09:36:23,132     706 |  sprintf(sub, "%03x/", i);
2021-07-10T09:36:23,132         |               ^~~~~~~
2021-07-10T09:36:23,132   In file included from /usr/include/stdio.h:867,
2021-07-10T09:36:23,133                    from mdtraj/formats/dtr/include/molfile_plugin.h:35,
2021-07-10T09:36:23,133                    from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
2021-07-10T09:36:23,133                    from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
2021-07-10T09:36:23,133   /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6
2021-07-10T09:36:23,133      36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
2021-07-10T09:36:23,133         |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:23,133      37 |       __bos (__s), __fmt, __va_arg_pack ());
2021-07-10T09:36:23,133         |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:23,134   mdtraj/formats/dtr/src/dtrplugin.cxx:714:23: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=]
2021-07-10T09:36:23,134     714 |      sprintf(subsub, "%03x", j);
2021-07-10T09:36:23,134         |                       ^~~~
2021-07-10T09:36:23,134   mdtraj/formats/dtr/src/dtrplugin.cxx:714:22: note: directive argument in the range [0, 2147483646]
2021-07-10T09:36:23,134     714 |      sprintf(subsub, "%03x", j);
2021-07-10T09:36:23,134         |                      ^~~~~~
2021-07-10T09:36:23,134   In file included from /usr/include/stdio.h:867,
2021-07-10T09:36:23,135                    from mdtraj/formats/dtr/include/molfile_plugin.h:35,
2021-07-10T09:36:23,135                    from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
2021-07-10T09:36:23,135                    from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
2021-07-10T09:36:23,135   /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6
2021-07-10T09:36:23,135      36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
2021-07-10T09:36:23,135         |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:23,135      37 |       __bos (__s), __fmt, __va_arg_pack ());
2021-07-10T09:36:23,135         |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:23,541   mdtraj/formats/dtr/src/dtrplugin.cxx: In function ‘std::string framefile(const string&, size_t, size_t, int, int)’:
2021-07-10T09:36:23,542   mdtraj/formats/dtr/src/dtrplugin.cxx:667:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
2021-07-10T09:36:23,542     667 |      sprintf(answer, "%03x/", d1);
2021-07-10T09:36:23,542         |                            ^
2021-07-10T09:36:23,542   In file included from /usr/include/stdio.h:867,
2021-07-10T09:36:23,542                    from mdtraj/formats/dtr/include/molfile_plugin.h:35,
2021-07-10T09:36:23,542                    from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
2021-07-10T09:36:23,543                    from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
2021-07-10T09:36:23,543   /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9
2021-07-10T09:36:23,543      36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
2021-07-10T09:36:23,543         |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:23,543      37 |       __bos (__s), __fmt, __va_arg_pack ());
2021-07-10T09:36:23,543         |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:23,543   mdtraj/formats/dtr/src/dtrplugin.cxx:665:28: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=]
2021-07-10T09:36:23,544     665 |      sprintf(answer, "%03x/%03x/", d1, d2);
2021-07-10T09:36:23,544         |                            ^~~~
2021-07-10T09:36:23,544   mdtraj/formats/dtr/src/dtrplugin.cxx:665:22: note: directive argument in the range [0, 2147483646]
2021-07-10T09:36:23,544     665 |      sprintf(answer, "%03x/%03x/", d1, d2);
2021-07-10T09:36:23,544         |                      ^~~~~~~~~~~~
2021-07-10T09:36:23,544   In file included from /usr/include/stdio.h:867,
2021-07-10T09:36:23,544                    from mdtraj/formats/dtr/include/molfile_plugin.h:35,
2021-07-10T09:36:23,544                    from mdtraj/formats/dtr/include/dtrplugin.hxx:46,
2021-07-10T09:36:23,545                    from mdtraj/formats/dtr/src/dtrplugin.cxx:42:
2021-07-10T09:36:23,545   /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9
2021-07-10T09:36:23,545      36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
2021-07-10T09:36:23,545         |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:23,545      37 |       __bos (__s), __fmt, __va_arg_pack ());
2021-07-10T09:36:23,545         |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-10T09:36:31,447   arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/dtr.o build/temp.linux-armv7l-3.9/mdtraj/formats/dtr/src/dtrplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/dtr.cpython-39-arm-linux-gnueabihf.so
2021-07-10T09:36:31,858   building 'mdtraj._rmsd' extension
2021-07-10T09:36:31,858   creating build/temp.linux-armv7l-3.9/mdtraj/rmsd
2021-07-10T09:36:31,859   creating build/temp.linux-armv7l-3.9/mdtraj/rmsd/src
2021-07-10T09:36:31,860   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Imdtraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c mdtraj/rmsd/_rmsd.c -o build/temp.linux-armv7l-3.9/mdtraj/rmsd/_rmsd.o -fopenmp -msse2 -O3 -funroll-loops
2021-07-10T09:36:31,878   arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’
2021-07-10T09:36:31,880   error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1
2021-07-10T09:36:32,414   Building wheel for mdtraj (setup.py): finished with status 'error'
2021-07-10T09:36:32,415   ERROR: Failed building wheel for mdtraj
2021-07-10T09:36:32,415   Running setup.py clean for mdtraj
2021-07-10T09:36:32,416   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-m_grhd85/mdtraj_da341428ac044944af06015aa51410ac/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
2021-07-10T09:36:33,368   C compiler:
2021-07-10T09:36:33,375   Using built-in specs.
2021-07-10T09:36:33,376   COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc
2021-07-10T09:36:33,376   COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper
2021-07-10T09:36:33,376   Target: arm-linux-gnueabihf
2021-07-10T09:36:33,376   Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6 --with-fpu=vfp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
2021-07-10T09:36:33,376   Thread model: posix
2021-07-10T09:36:33,376   Supported LTO compression algorithms: zlib zstd
2021-07-10T09:36:33,377   gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
2021-07-10T09:36:33,923   Attempting to autodetect OpenMP support... Compiler supports OpenMP
2021-07-10T09:36:34,106   Attempting to autodetect SSE3   support... Did not detect SSE3 support
2021-07-10T09:36:34,279   Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support

2021-07-10T09:36:34,494   running clean
2021-07-10T09:36:34,497   removing 'build/temp.linux-armv7l-3.9' (and everything under it)
2021-07-10T09:36:34,527   removing 'build/lib.linux-armv7l-3.9' (and everything under it)
2021-07-10T09:36:34,894   'build/bdist.linux-armv7l' does not exist -- can't clean it
2021-07-10T09:36:34,895   'build/scripts-3.9' does not exist -- can't clean it
2021-07-10T09:36:34,895   removing 'build'
2021-07-10T09:36:34,971 Failed to build mdtraj
2021-07-10T09:36:34,972 ERROR: Failed to build one or more wheels
2021-07-10T09:36:34,972 Exception information:
2021-07-10T09:36:34,972 Traceback (most recent call last):
2021-07-10T09:36:34,972   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main
2021-07-10T09:36:34,972     status = self.run(options, args)
2021-07-10T09:36:34,972   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
2021-07-10T09:36:34,972     return func(self, options, args)
2021-07-10T09:36:34,972   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run
2021-07-10T09:36:34,972     raise CommandError(
2021-07-10T09:36:34,972 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2021-07-10T09:36:34,976 Removed build tracker: '/tmp/pip-req-tracker-mvoifg0p'