2021-07-09T20:01:23,070 Created temporary directory: /tmp/pip-ephem-wheel-cache-jnrkocgu
2021-07-09T20:01:23,073 Created temporary directory: /tmp/pip-req-tracker-jau_1hs0
2021-07-09T20:01:23,074 Initialized build tracking at /tmp/pip-req-tracker-jau_1hs0
2021-07-09T20:01:23,074 Created build tracker: /tmp/pip-req-tracker-jau_1hs0
2021-07-09T20:01:23,074 Entered build tracker: /tmp/pip-req-tracker-jau_1hs0
2021-07-09T20:01:23,075 Created temporary directory: /tmp/pip-wheel-rm9cspv0
2021-07-09T20:01:23,107 1 location(s) to search for versions of mdtraj:
2021-07-09T20:01:23,107 * https://pypi.org/simple/mdtraj/
2021-07-09T20:01:23,108 Fetching project page and analyzing links: https://pypi.org/simple/mdtraj/
2021-07-09T20:01:23,108 Getting page https://pypi.org/simple/mdtraj/
2021-07-09T20:01:23,110 Found index url https://pypi.org/simple
2021-07-09T20:01:23,231   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
2021-07-09T20:01:23,232   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
2021-07-09T20:01:23,232   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/)
2021-07-09T20:01:23,232   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
2021-07-09T20:01:23,233   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
2021-07-09T20:01:23,233   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
2021-07-09T20:01:23,233   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/)
2021-07-09T20:01:23,233   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/)
2021-07-09T20:01:23,234   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/)
2021-07-09T20:01:23,234   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/)
2021-07-09T20:01:23,234   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
2021-07-09T20:01:23,234   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
2021-07-09T20:01:23,235   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/)
2021-07-09T20:01:23,235   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/)
2021-07-09T20:01:23,235   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/)
2021-07-09T20:01:23,235   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
2021-07-09T20:01:23,236   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
2021-07-09T20:01:23,236   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
2021-07-09T20:01:23,236   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
2021-07-09T20:01:23,236   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
2021-07-09T20:01:23,237   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
2021-07-09T20:01:23,237   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
2021-07-09T20:01:23,237   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
2021-07-09T20:01:23,237   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
2021-07-09T20:01:23,238   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
2021-07-09T20:01:23,238   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
2021-07-09T20:01:23,238   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
2021-07-09T20:01:23,238   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/)
2021-07-09T20:01:23,239   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
2021-07-09T20:01:23,239   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
2021-07-09T20:01:23,239   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
2021-07-09T20:01:23,239   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
2021-07-09T20:01:23,240   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
2021-07-09T20:01:23,255   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/)
2021-07-09T20:01:23,256   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/)
2021-07-09T20:01:23,257   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/)
2021-07-09T20:01:23,257   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
2021-07-09T20:01:23,257   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
2021-07-09T20:01:23,257   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
2021-07-09T20:01:23,258   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
2021-07-09T20:01:23,258   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
2021-07-09T20:01:23,258   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
2021-07-09T20:01:23,259   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
2021-07-09T20:01:23,259   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
2021-07-09T20:01:23,259   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
2021-07-09T20:01:23,259   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
2021-07-09T20:01:23,260   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
2021-07-09T20:01:23,260   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
2021-07-09T20:01:23,260   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/)
2021-07-09T20:01:23,261   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/)
2021-07-09T20:01:23,261   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/)
2021-07-09T20:01:23,262   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
2021-07-09T20:01:23,262   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
2021-07-09T20:01:23,262   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
2021-07-09T20:01:23,263   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
2021-07-09T20:01:23,263   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
2021-07-09T20:01:23,263   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
2021-07-09T20:01:23,263   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
2021-07-09T20:01:23,264   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
2021-07-09T20:01:23,264   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
2021-07-09T20:01:23,264   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
2021-07-09T20:01:23,264   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
2021-07-09T20:01:23,265   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
2021-07-09T20:01:23,265   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
2021-07-09T20:01:23,265   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
2021-07-09T20:01:23,266   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/)
2021-07-09T20:01:23,266   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/)
2021-07-09T20:01:23,267   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/)
2021-07-09T20:01:23,267   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/)
2021-07-09T20:01:23,267   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
2021-07-09T20:01:23,268   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/)
2021-07-09T20:01:23,268   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/)
2021-07-09T20:01:23,269   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/)
2021-07-09T20:01:23,269   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/)
2021-07-09T20:01:23,270   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
2021-07-09T20:01:23,270 Skipping link: not a file: https://pypi.org/simple/mdtraj/
2021-07-09T20:01:23,278 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates
2021-07-09T20:01:23,296 Collecting mdtraj==0.5.1
2021-07-09T20:01:23,297   Created temporary directory: /tmp/pip-unpack-h9s1rgtv
2021-07-09T20:01:24,348   Downloading mdtraj-0.5.1.zip (3.1 MB)
2021-07-09T20:01:25,701   Added mdtraj==0.5.1 from https://files.pythonhosted.org/packages/07/17/04c7422cc1092ca74b51da1f9ba4f76e38b53ef6f35bf4ad4bb65301c316/mdtraj-0.5.1.zip#sha256=258a81b7b500493e36ea590f7222ae06df4782a6d5de4d04a3569a831a98584b to build tracker '/tmp/pip-req-tracker-jau_1hs0'
2021-07-09T20:01:25,702     Running setup.py (path:/tmp/pip-wheel-rm9cspv0/mdtraj_fb40759775e54c2984254970ca458555/setup.py) egg_info for package mdtraj
2021-07-09T20:01:25,703     Created temporary directory: /tmp/pip-pip-egg-info-f7stqvcu
2021-07-09T20:01:25,703     Running command python setup.py egg_info
2021-07-09T20:01:27,378     Attempting to autodetect OpenMP support... Compiler supports OpenMP
2021-07-09T20:01:27,379     running egg_info
2021-07-09T20:01:27,380     creating /tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info
2021-07-09T20:01:27,381     writing /tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info/PKG-INFO
2021-07-09T20:01:27,383     writing dependency_links to /tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info/dependency_links.txt
2021-07-09T20:01:27,385     writing entry points to /tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info/entry_points.txt
2021-07-09T20:01:27,386     writing requirements to /tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info/requires.txt
2021-07-09T20:01:27,387     writing top-level names to /tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info/top_level.txt
2021-07-09T20:01:27,389     writing manifest file '/tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info/SOURCES.txt'
2021-07-09T20:01:27,552     reading manifest file '/tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info/SOURCES.txt'
2021-07-09T20:01:27,554     reading manifest template 'MANIFEST.in'
2021-07-09T20:01:27,604     writing manifest file '/tmp/pip-pip-egg-info-f7stqvcu/mdtraj.egg-info/SOURCES.txt'
2021-07-09T20:01:27,710   Source in /tmp/pip-wheel-rm9cspv0/mdtraj_fb40759775e54c2984254970ca458555 has version 0.5.1, which satisfies requirement mdtraj==0.5.1 from https://files.pythonhosted.org/packages/07/17/04c7422cc1092ca74b51da1f9ba4f76e38b53ef6f35bf4ad4bb65301c316/mdtraj-0.5.1.zip#sha256=258a81b7b500493e36ea590f7222ae06df4782a6d5de4d04a3569a831a98584b
2021-07-09T20:01:27,711   Removed mdtraj==0.5.1 from https://files.pythonhosted.org/packages/07/17/04c7422cc1092ca74b51da1f9ba4f76e38b53ef6f35bf4ad4bb65301c316/mdtraj-0.5.1.zip#sha256=258a81b7b500493e36ea590f7222ae06df4782a6d5de4d04a3569a831a98584b from build tracker '/tmp/pip-req-tracker-jau_1hs0'
2021-07-09T20:01:27,715 Created temporary directory: /tmp/pip-unpack-1049krpm
2021-07-09T20:01:27,716 Building wheels for collected packages: mdtraj
2021-07-09T20:01:27,720   Created temporary directory: /tmp/pip-wheel-hlxih1uy
2021-07-09T20:01:27,721   Building wheel for mdtraj (setup.py): started
2021-07-09T20:01:27,721   Destination directory: /tmp/pip-wheel-hlxih1uy
2021-07-09T20:01:27,721   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-rm9cspv0/mdtraj_fb40759775e54c2984254970ca458555/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-rm9cspv0/mdtraj_fb40759775e54c2984254970ca458555/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-hlxih1uy
2021-07-09T20:01:29,148   Attempting to autodetect OpenMP support... Compiler supports OpenMP
2021-07-09T20:01:29,357   running bdist_wheel
2021-07-09T20:01:29,362   running build
2021-07-09T20:01:29,362   running build_py
2021-07-09T20:01:29,497   creating build
2021-07-09T20:01:29,497   creating build/lib.linux-armv7l-3.9
2021-07-09T20:01:29,498   creating build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,499   copying MDTraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,501   copying MDTraj/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,503   copying MDTraj/arc.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,505   copying MDTraj/lh5.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,507   copying MDTraj/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,510   copying MDTraj/topology.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,512   copying MDTraj/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,515   copying MDTraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,517   copying MDTraj/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,522   copying MDTraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj
2021-07-09T20:01:29,526   creating build/lib.linux-armv7l-3.9/mdtraj/pdb
2021-07-09T20:01:29,526   copying MDTraj/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb
2021-07-09T20:01:29,530   copying MDTraj/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb
2021-07-09T20:01:29,533   copying MDTraj/pdb/element.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb
2021-07-09T20:01:29,536   copying MDTraj/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb
2021-07-09T20:01:29,538   copying MDTraj/pdb/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/pdb
2021-07-09T20:01:29,540   creating build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-09T20:01:29,541   copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-09T20:01:29,543   copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-09T20:01:29,545   copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-09T20:01:29,547   copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-09T20:01:29,550   copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing
2021-07-09T20:01:29,553   creating build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,554   copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,557   copying MDTraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,559   copying MDTraj/utils/ffi.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,561   copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,562   copying MDTraj/utils/six.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,565   copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,567   copying MDTraj/utils/arrays.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,569   copying MDTraj/utils/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils
2021-07-09T20:01:29,573   creating build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-09T20:01:29,574   copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-09T20:01:29,576   copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-09T20:01:29,578   copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-09T20:01:29,580   copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-09T20:01:29,582   copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters
2021-07-09T20:01:29,585   creating build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,586   copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,589   copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,591   copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,593   copying MDTraj/geometry/hbond.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,595   copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,598   copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,601   copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,603   copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,605   copying MDTraj/geometry/sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry
2021-07-09T20:01:29,608   creating build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,609   copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,612   copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,613   copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,616   copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,618   copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,620   copying MDTraj/tests/test_lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,622   copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,625   copying MDTraj/tests/test_topology.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,627   copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,629   copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,631   copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,633   copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,635   copying MDTraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,637   copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,638   copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,641   copying MDTraj/tests/test_arc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,643   copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests
2021-07-09T20:01:29,646   creating build/lib.linux-armv7l-3.9/mdtraj/scripts
2021-07-09T20:01:29,647   copying scripts/mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts
2021-07-09T20:01:29,649   copying scripts/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts
2021-07-09T20:01:29,651   copying scripts/mdinspect.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts
2021-07-09T20:01:29,659   creating build/lib.linux-armv7l-3.9/mdtraj/pdb/data
2021-07-09T20:01:29,660   copying MDTraj/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/pdb/data
2021-07-09T20:01:29,663   copying MDTraj/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/pdb/data
2021-07-09T20:01:29,666   creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,667   copying MDTraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,669   copying MDTraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,672   copying MDTraj/testing/reference/native.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,674   copying MDTraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,676   copying MDTraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,681   copying MDTraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,683   copying MDTraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,689   copying MDTraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,703   copying MDTraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,717   copying MDTraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,726   copying MDTraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,728   copying MDTraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,730   copying MDTraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,736   copying MDTraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,743   copying MDTraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,761   copying MDTraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,766   copying MDTraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,770   copying MDTraj/testing/reference/native2.xml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,773   copying MDTraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,783   copying MDTraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,808   copying MDTraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,825   copying MDTraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,831   copying MDTraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,840   copying MDTraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,845   copying MDTraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,850   copying MDTraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,874   copying MDTraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,879   copying MDTraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,881   copying MDTraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,884   copying MDTraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,888   copying MDTraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,892   copying MDTraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference
2021-07-09T20:01:29,949   running build_ext
2021-07-09T20:01:30,010   skipping 'MDTraj/xtc/xtc.c' Cython extension (up-to-date)
2021-07-09T20:01:30,010   skipping 'MDTraj/xtc/trr.c' Cython extension (up-to-date)
2021-07-09T20:01:30,011   skipping 'MDTraj/dcd/dcd.c' Cython extension (up-to-date)
2021-07-09T20:01:30,011   skipping 'MDTraj/binpos/binpos.c' Cython extension (up-to-date)
2021-07-09T20:01:30,012   skipping 'MDTraj/rmsd/_rmsd.c' Cython extension (up-to-date)
2021-07-09T20:01:30,012   building 'mdtraj.xtc' extension
2021-07-09T20:01:30,012   creating build/temp.linux-armv7l-3.9
2021-07-09T20:01:30,013   creating build/temp.linux-armv7l-3.9/MDTraj
2021-07-09T20:01:30,013   creating build/temp.linux-armv7l-3.9/MDTraj/xtc
2021-07-09T20:01:30,014   creating build/temp.linux-armv7l-3.9/MDTraj/xtc/src
2021-07-09T20:01:30,015   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/xtc/include/ -IMDTraj/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile.o
2021-07-09T20:01:30,169   MDTraj/xtc/src/xdrfile.c: In function ‘sizeofint’:
2021-07-09T20:01:30,169   MDTraj/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:30,169     478 |     while (size >= num && num_of_bits < 32)
2021-07-09T20:01:30,169         |                 ^~
2021-07-09T20:01:30,169   MDTraj/xtc/src/xdrfile.c: In function ‘sizeofints’:
2021-07-09T20:01:30,170   MDTraj/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,170     524 |     while (bytes[num_of_bytes] >= num)
2021-07-09T20:01:30,170         |                                ^~
2021-07-09T20:01:30,170   MDTraj/xtc/src/xdrfile.c: In function ‘encodeints’:
2021-07-09T20:01:30,171   MDTraj/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:30,171     633 |     if (num_of_bits >= num_of_bytes * 8)
2021-07-09T20:01:30,171         |                     ^~
2021-07-09T20:01:30,171   MDTraj/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:30,171     635 |   for (i = 0; i < num_of_bytes; i++)
2021-07-09T20:01:30,171         |                 ^
2021-07-09T20:01:30,172   MDTraj/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:30,172     643 |   for (i = 0; i < num_of_bytes-1; i++)
2021-07-09T20:01:30,172         |                 ^
2021-07-09T20:01:30,172   MDTraj/xtc/src/xdrfile.c: In function ‘decodebits’:
2021-07-09T20:01:30,172   MDTraj/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,172     683 |   if (lastbits < num_of_bits)
2021-07-09T20:01:30,172         |                ^
2021-07-09T20:01:30,173   MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
2021-07-09T20:01:30,174   MDTraj/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,174     797 |  if(size3>xfp->buf1size)
2021-07-09T20:01:30,174         |          ^
2021-07-09T20:01:30,175   MDTraj/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,175     851 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:30,175         |                   ^
2021-07-09T20:01:30,176   MDTraj/xtc/src/xdrfile.c:851:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-09T20:01:30,176     851 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:30,176         |                                     ^~~
2021-07-09T20:01:30,178   MDTraj/xtc/src/xdrfile.c:771:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:30,178     771 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-09T20:01:30,178         |                         ^~~~~~
2021-07-09T20:01:30,178   MDTraj/xtc/src/xdrfile.c:768:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:30,178     768 |  int smallidx, minidx, maxidx;
2021-07-09T20:01:30,178         |                ^~~~~~
2021-07-09T20:01:30,179   MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
2021-07-09T20:01:30,179   MDTraj/xtc/src/xdrfile.c:999:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,179     999 |  if(size3>xfp->buf1size)
2021-07-09T20:01:30,179         |          ^
2021-07-09T20:01:30,184   MDTraj/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:30,184    1122 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
2021-07-09T20:01:30,184         |                  ^
2021-07-09T20:01:30,184   MDTraj/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,185    1128 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:30,185         |                   ^
2021-07-09T20:01:30,185   MDTraj/xtc/src/xdrfile.c:1128:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-09T20:01:30,185    1128 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:30,185         |                                     ^~~
2021-07-09T20:01:30,188   MDTraj/xtc/src/xdrfile.c:1260:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:30,189    1260 |  if(tmp==(unsigned int)buf2[0])
2021-07-09T20:01:30,189         |        ^~
2021-07-09T20:01:30,189   MDTraj/xtc/src/xdrfile.c:988:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:30,189     988 |  int errval=1;
2021-07-09T20:01:30,189         |      ^~~~~~
2021-07-09T20:01:30,190   MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
2021-07-09T20:01:30,190   MDTraj/xtc/src/xdrfile.c:1300:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,191    1300 |  if(size3>xfp->buf1size)
2021-07-09T20:01:30,191         |          ^
2021-07-09T20:01:30,192   MDTraj/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,193    1355 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:30,193         |                   ^
2021-07-09T20:01:30,193   MDTraj/xtc/src/xdrfile.c:1355:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-09T20:01:30,193    1355 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:30,193         |                                     ^~~
2021-07-09T20:01:30,196   MDTraj/xtc/src/xdrfile.c:1277:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:30,196    1277 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-09T20:01:30,196         |                         ^~~~~~
2021-07-09T20:01:30,197   MDTraj/xtc/src/xdrfile.c:1274:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:30,197    1274 |  int smallidx, minidx, maxidx;
2021-07-09T20:01:30,197         |                ^~~~~~
2021-07-09T20:01:30,197   MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
2021-07-09T20:01:30,198   MDTraj/xtc/src/xdrfile.c:1491:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,198    1491 |  if(size3>xfp->buf1size) {
2021-07-09T20:01:30,198         |          ^
2021-07-09T20:01:30,204   MDTraj/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:30,204    1606 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
2021-07-09T20:01:30,205         |                  ^
2021-07-09T20:01:30,205   MDTraj/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:30,205    1611 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:30,205         |                   ^
2021-07-09T20:01:30,206   MDTraj/xtc/src/xdrfile.c:1611:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-09T20:01:30,206    1611 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:30,206         |                                     ^~~
2021-07-09T20:01:30,209   MDTraj/xtc/src/xdrfile.c:1721:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:30,209    1721 |  if(tmp==(unsigned int)buf2[0])
2021-07-09T20:01:30,210         |        ^~
2021-07-09T20:01:30,210   MDTraj/xtc/src/xdrfile.c:1481:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:30,210    1481 |  int errval=1;
2021-07-09T20:01:30,210         |      ^~~~~~
2021-07-09T20:01:32,348   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/xtc/include/ -IMDTraj/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/xtc/src/xdrfile_xtc.c -o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile_xtc.o
2021-07-09T20:01:32,456   MDTraj/xtc/src/xdrfile_xtc.c: In function ‘xtc_coord’:
2021-07-09T20:01:32,456   MDTraj/xtc/src/xdrfile_xtc.c:51:8: warning: unused variable ‘j’ [-Wunused-variable]
2021-07-09T20:01:32,457      51 |  int i,j,result;
2021-07-09T20:01:32,457         |        ^
2021-07-09T20:01:32,457   MDTraj/xtc/src/xdrfile_xtc.c:51:6: warning: unused variable ‘i’ [-Wunused-variable]
2021-07-09T20:01:32,458      51 |  int i,j,result;
2021-07-09T20:01:32,458         |      ^
2021-07-09T20:01:32,584   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/xtc/include/ -IMDTraj/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/xtc/xtc.c -o build/temp.linux-armv7l-3.9/MDTraj/xtc/xtc.o
2021-07-09T20:01:32,973   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-09T20:01:32,974                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-09T20:01:32,974                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-09T20:01:32,974                    from MDTraj/xtc/xtc.c:314:
2021-07-09T20:01:32,974   /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]
2021-07-09T20:01:32,974      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-09T20:01:32,974         |  ^~~~~~~
2021-07-09T20:01:33,256   MDTraj/xtc/xtc.c: In function ‘__Pyx_ParseOptionalKeywords’:
2021-07-09T20:01:33,261   MDTraj/xtc/xtc.c:9567:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,261    9567 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,261         |                     ^
2021-07-09T20:01:33,262   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,262                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,262                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,263   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,263     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,263         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,269   MDTraj/xtc/xtc.c:9567:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,269    9567 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,269         |                     ^
2021-07-09T20:01:33,269   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,270                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,270                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,270   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:33,270     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:33,270         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,276   MDTraj/xtc/xtc.c:9567:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,276    9567 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,277         |                     ^
2021-07-09T20:01:33,277   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,277                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,277                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,277   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,277     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,277         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,284   MDTraj/xtc/xtc.c:9567:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,284    9567 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,284         |                     ^
2021-07-09T20:01:33,284   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,284                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,284                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,284   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,285     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,285         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,291   MDTraj/xtc/xtc.c:9567:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,291    9567 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,291         |                     ^
2021-07-09T20:01:33,291   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,292                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,292                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,292   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:33,292     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:33,292         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,298   MDTraj/xtc/xtc.c:9567:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,298    9567 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,298         |                     ^
2021-07-09T20:01:33,299   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,299                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,299                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,299   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,299     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,299         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,307   MDTraj/xtc/xtc.c:9583:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,307    9583 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,307         |                         ^
2021-07-09T20:01:33,307   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,308                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,308                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,308   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,308     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,308         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,314   MDTraj/xtc/xtc.c:9583:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,314    9583 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,314         |                         ^
2021-07-09T20:01:33,315   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,315                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,315                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,315   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:33,315     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:33,315         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,321   MDTraj/xtc/xtc.c:9583:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,322    9583 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,322         |                         ^
2021-07-09T20:01:33,322   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,322                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,322                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,322   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,322     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,323         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,329   MDTraj/xtc/xtc.c:9583:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,329    9583 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,329         |                         ^
2021-07-09T20:01:33,329   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,329                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,330                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,330   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,330     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,330         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,336   MDTraj/xtc/xtc.c:9583:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,336    9583 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,336         |                         ^
2021-07-09T20:01:33,337   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,337                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,337                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,337   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:33,337     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:33,337         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,343   MDTraj/xtc/xtc.c:9583:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,343    9583 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:33,344         |                         ^
2021-07-09T20:01:33,344   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,344                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,344                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,344   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,344     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,344         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,363   MDTraj/xtc/xtc.c: In function ‘__Pyx_Raise’:
2021-07-09T20:01:33,368   MDTraj/xtc/xtc.c:9789:9: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,368    9789 |         owned_instance = PyEval_CallObject(type, args);
2021-07-09T20:01:33,368         |         ^~~~~~~~~~~~~~
2021-07-09T20:01:33,369   In file included from /usr/include/python3.9/Python.h:145,
2021-07-09T20:01:33,369                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,369   /usr/include/python3.9/ceval.h:17:43: note: declared here
2021-07-09T20:01:33,369      17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
2021-07-09T20:01:33,369         |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,529   MDTraj/xtc/xtc.c: In function ‘__Pyx_PyObject_AsStringAndSize’:
2021-07-09T20:01:33,536   MDTraj/xtc/xtc.c:11999:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,536   11999 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:33,536         |             ^
2021-07-09T20:01:33,536   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,537                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,537                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,537   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,537     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,537         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,545   MDTraj/xtc/xtc.c:11999:13: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,545   11999 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:33,545         |             ^
2021-07-09T20:01:33,545   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,545                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,546                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,546   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:33,546     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:33,546         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,553   MDTraj/xtc/xtc.c:11999:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:33,554   11999 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:33,554         |             ^
2021-07-09T20:01:33,554   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:33,554                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:33,554                    from MDTraj/xtc/xtc.c:16:
2021-07-09T20:01:33,554   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:33,555     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:33,555         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:33,561   MDTraj/xtc/xtc.c:12000:20: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-09T20:01:33,561   12000 |             return PyUnicode_AsUTF8(o);
2021-07-09T20:01:33,562         |                    ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:35,476   MDTraj/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_3xtc_17XTCTrajectoryFile_14_write’:
2021-07-09T20:01:35,476   MDTraj/xtc/xtc.c:196:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-09T20:01:35,476     196 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-09T20:01:35,476         |                                        ^~~~~~~~~~~~~~~
2021-07-09T20:01:35,480   MDTraj/xtc/xtc.c:5580:7: note: ‘__pyx_v_status’ was declared here
2021-07-09T20:01:35,480    5580 |   int __pyx_v_status;
2021-07-09T20:01:35,480         |       ^~~~~~~~~~~~~~
2021-07-09T20:01:43,126   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/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-3.9/MDTraj/xtc/xtc.o -o build/lib.linux-armv7l-3.9/mdtraj/xtc.cpython-39-arm-linux-gnueabihf.so
2021-07-09T20:01:43,293   building 'mdtraj.trr' extension
2021-07-09T20:01:43,293   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/xtc/include/ -IMDTraj/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile.o
2021-07-09T20:01:43,448   MDTraj/xtc/src/xdrfile.c: In function ‘sizeofint’:
2021-07-09T20:01:43,449   MDTraj/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:43,449     478 |     while (size >= num && num_of_bits < 32)
2021-07-09T20:01:43,449         |                 ^~
2021-07-09T20:01:43,450   MDTraj/xtc/src/xdrfile.c: In function ‘sizeofints’:
2021-07-09T20:01:43,450   MDTraj/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,450     524 |     while (bytes[num_of_bytes] >= num)
2021-07-09T20:01:43,450         |                                ^~
2021-07-09T20:01:43,452   MDTraj/xtc/src/xdrfile.c: In function ‘encodeints’:
2021-07-09T20:01:43,452   MDTraj/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:43,452     633 |     if (num_of_bits >= num_of_bytes * 8)
2021-07-09T20:01:43,453         |                     ^~
2021-07-09T20:01:43,453   MDTraj/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:43,453     635 |   for (i = 0; i < num_of_bytes; i++)
2021-07-09T20:01:43,453         |                 ^
2021-07-09T20:01:43,454   MDTraj/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:43,454     643 |   for (i = 0; i < num_of_bytes-1; i++)
2021-07-09T20:01:43,454         |                 ^
2021-07-09T20:01:43,455   MDTraj/xtc/src/xdrfile.c: In function ‘decodebits’:
2021-07-09T20:01:43,455   MDTraj/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,456     683 |   if (lastbits < num_of_bits)
2021-07-09T20:01:43,456         |                ^
2021-07-09T20:01:43,457   MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
2021-07-09T20:01:43,458   MDTraj/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,458     797 |  if(size3>xfp->buf1size)
2021-07-09T20:01:43,458         |          ^
2021-07-09T20:01:43,460   MDTraj/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,460     851 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:43,460         |                   ^
2021-07-09T20:01:43,462   MDTraj/xtc/src/xdrfile.c:851:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-09T20:01:43,462     851 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:43,462         |                                     ^~~
2021-07-09T20:01:43,464   MDTraj/xtc/src/xdrfile.c:771:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:43,465     771 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-09T20:01:43,465         |                         ^~~~~~
2021-07-09T20:01:43,465   MDTraj/xtc/src/xdrfile.c:768:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:43,465     768 |  int smallidx, minidx, maxidx;
2021-07-09T20:01:43,465         |                ^~~~~~
2021-07-09T20:01:43,466   MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
2021-07-09T20:01:43,467   MDTraj/xtc/src/xdrfile.c:999:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,467     999 |  if(size3>xfp->buf1size)
2021-07-09T20:01:43,467         |          ^
2021-07-09T20:01:43,472   MDTraj/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:43,472    1122 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
2021-07-09T20:01:43,472         |                  ^
2021-07-09T20:01:43,473   MDTraj/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,473    1128 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:43,473         |                   ^
2021-07-09T20:01:43,474   MDTraj/xtc/src/xdrfile.c:1128:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-09T20:01:43,474    1128 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:43,474         |                                     ^~~
2021-07-09T20:01:43,477   MDTraj/xtc/src/xdrfile.c:1260:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:43,478    1260 |  if(tmp==(unsigned int)buf2[0])
2021-07-09T20:01:43,478         |        ^~
2021-07-09T20:01:43,478   MDTraj/xtc/src/xdrfile.c:988:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:43,479     988 |  int errval=1;
2021-07-09T20:01:43,479         |      ^~~~~~
2021-07-09T20:01:43,480   MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
2021-07-09T20:01:43,481   MDTraj/xtc/src/xdrfile.c:1300:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,481    1300 |  if(size3>xfp->buf1size)
2021-07-09T20:01:43,481         |          ^
2021-07-09T20:01:43,483   MDTraj/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,483    1355 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:43,483         |                   ^
2021-07-09T20:01:43,484   MDTraj/xtc/src/xdrfile.c:1355:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-09T20:01:43,484    1355 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:43,485         |                                     ^~~
2021-07-09T20:01:43,487   MDTraj/xtc/src/xdrfile.c:1277:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:43,488    1277 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-09T20:01:43,488         |                         ^~~~~~
2021-07-09T20:01:43,489   MDTraj/xtc/src/xdrfile.c:1274:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:43,489    1274 |  int smallidx, minidx, maxidx;
2021-07-09T20:01:43,489         |                ^~~~~~
2021-07-09T20:01:43,490   MDTraj/xtc/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
2021-07-09T20:01:43,491   MDTraj/xtc/src/xdrfile.c:1491:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,491    1491 |  if(size3>xfp->buf1size) {
2021-07-09T20:01:43,491         |          ^
2021-07-09T20:01:43,497   MDTraj/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:43,497    1606 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
2021-07-09T20:01:43,498         |                  ^
2021-07-09T20:01:43,499   MDTraj/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:01:43,499    1611 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:43,499         |                   ^
2021-07-09T20:01:43,500   MDTraj/xtc/src/xdrfile.c:1611:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-09T20:01:43,500    1611 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-09T20:01:43,500         |                                     ^~~
2021-07-09T20:01:43,504   MDTraj/xtc/src/xdrfile.c:1721:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:01:43,504    1721 |  if(tmp==(unsigned int)buf2[0])
2021-07-09T20:01:43,504         |        ^~
2021-07-09T20:01:43,505   MDTraj/xtc/src/xdrfile.c:1481:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-09T20:01:43,505    1481 |  int errval=1;
2021-07-09T20:01:43,505         |      ^~~~~~
2021-07-09T20:01:45,647   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/xtc/include/ -IMDTraj/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/xtc/src/xdrfile_trr.c -o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile_trr.o
2021-07-09T20:01:45,748   MDTraj/xtc/src/xdrfile_trr.c: In function ‘do_trnheader’:
2021-07-09T20:01:45,749   MDTraj/xtc/src/xdrfile_trr.c:93:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-09T20:01:45,749      93 |         if (slen != strlen(version)+1)
2021-07-09T20:01:45,749         |                  ^~
2021-07-09T20:01:45,749   MDTraj/xtc/src/xdrfile_trr.c:103:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-09T20:01:45,749     103 |         if (xdrfile_write_string(version,xd) != (strlen(version)+1) )
2021-07-09T20:01:45,749         |                                              ^~
2021-07-09T20:01:46,307   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/xtc/include/ -IMDTraj/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/xtc/trr.c -o build/temp.linux-armv7l-3.9/MDTraj/xtc/trr.o
2021-07-09T20:01:46,692   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-09T20:01:46,692                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-09T20:01:46,692                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-09T20:01:46,692                    from MDTraj/xtc/trr.c:314:
2021-07-09T20:01:46,692   /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]
2021-07-09T20:01:46,693      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-09T20:01:46,693         |  ^~~~~~~
2021-07-09T20:01:46,974   MDTraj/xtc/trr.c: In function ‘__Pyx_ParseOptionalKeywords’:
2021-07-09T20:01:46,979   MDTraj/xtc/trr.c:9554:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:46,979    9554 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:46,980         |                     ^
2021-07-09T20:01:46,980   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:46,980                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:46,980                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:46,980   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:46,980     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:46,980         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:46,986   MDTraj/xtc/trr.c:9554:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:46,986    9554 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:46,986         |                     ^
2021-07-09T20:01:46,986   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:46,987                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:46,987                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:46,987   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:46,987     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:46,987         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:46,992   MDTraj/xtc/trr.c:9554:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:46,992    9554 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:46,992         |                     ^
2021-07-09T20:01:46,992   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:46,993                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:46,993                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:46,993   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:46,993     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:46,993         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:46,998   MDTraj/xtc/trr.c:9554:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:46,998    9554 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:46,998         |                     ^
2021-07-09T20:01:46,998   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:46,999                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:46,999                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:46,999   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:46,999     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:46,999         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,004   MDTraj/xtc/trr.c:9554:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,004    9554 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:47,004         |                     ^
2021-07-09T20:01:47,004   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,005                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,005                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,005   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:47,005     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:47,005         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,010   MDTraj/xtc/trr.c:9554:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,010    9554 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:47,010         |                     ^
2021-07-09T20:01:47,010   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,011                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,011                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,011   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:47,011     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:47,011         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,017   MDTraj/xtc/trr.c:9570:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,018    9570 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:47,018         |                         ^
2021-07-09T20:01:47,018   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,018                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,018                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,018   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:47,018     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:47,018         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,023   MDTraj/xtc/trr.c:9570:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,024    9570 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:47,024         |                         ^
2021-07-09T20:01:47,024   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,024                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,024                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,024   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:47,024     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:47,024         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,029   MDTraj/xtc/trr.c:9570:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,029    9570 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:47,030         |                         ^
2021-07-09T20:01:47,030   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,030                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,030                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,030   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:47,030     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:47,030         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,035   MDTraj/xtc/trr.c:9570:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,036    9570 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:47,036         |                         ^
2021-07-09T20:01:47,036   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,036                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,036                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,036   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:47,036     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:47,036         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,041   MDTraj/xtc/trr.c:9570:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,042    9570 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:47,042         |                         ^
2021-07-09T20:01:47,042   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,042                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,042                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,042   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:47,042     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:47,042         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,047   MDTraj/xtc/trr.c:9570:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,048    9570 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:47,048         |                         ^
2021-07-09T20:01:47,048   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,048                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,048                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,048   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:47,048     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:47,048         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,065   MDTraj/xtc/trr.c: In function ‘__Pyx_Raise’:
2021-07-09T20:01:47,070   MDTraj/xtc/trr.c:9776:9: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,071    9776 |         owned_instance = PyEval_CallObject(type, args);
2021-07-09T20:01:47,071         |         ^~~~~~~~~~~~~~
2021-07-09T20:01:47,071   In file included from /usr/include/python3.9/Python.h:145,
2021-07-09T20:01:47,071                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,071   /usr/include/python3.9/ceval.h:17:43: note: declared here
2021-07-09T20:01:47,071      17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
2021-07-09T20:01:47,072         |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,233   MDTraj/xtc/trr.c: In function ‘__Pyx_PyObject_AsStringAndSize’:
2021-07-09T20:01:47,239   MDTraj/xtc/trr.c:11993:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,239   11993 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:47,239         |             ^
2021-07-09T20:01:47,239   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,239                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,240                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,240   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:47,240     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:47,240         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,246   MDTraj/xtc/trr.c:11993:13: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,247   11993 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:47,247         |             ^
2021-07-09T20:01:47,247   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,247                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,247                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,247   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:47,247     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:47,248         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,254   MDTraj/xtc/trr.c:11993:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:47,254   11993 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:47,254         |             ^
2021-07-09T20:01:47,254   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:47,255                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:47,255                    from MDTraj/xtc/trr.c:16:
2021-07-09T20:01:47,255   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:47,255     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:47,255         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:47,260   MDTraj/xtc/trr.c:11994:20: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-09T20:01:47,261   11994 |             return PyUnicode_AsUTF8(o);
2021-07-09T20:01:47,261         |                    ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:49,044   MDTraj/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_3trr_17TRRTrajectoryFile_14_write’:
2021-07-09T20:01:49,044   MDTraj/xtc/trr.c:196:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-09T20:01:49,044     196 |   #define PyInt_FromLong               PyLong_FromLong
2021-07-09T20:01:49,044         |                                        ^~~~~~~~~~~~~~~
2021-07-09T20:01:49,047   MDTraj/xtc/trr.c:5578:7: note: ‘__pyx_v_status’ was declared here
2021-07-09T20:01:49,047    5578 |   int __pyx_v_status;
2021-07-09T20:01:49,047         |       ^~~~~~~~~~~~~~
2021-07-09T20:01:56,925   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/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/MDTraj/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-3.9/MDTraj/xtc/trr.o -o build/lib.linux-armv7l-3.9/mdtraj/trr.cpython-39-arm-linux-gnueabihf.so
2021-07-09T20:01:57,082   building 'mdtraj.dcd' extension
2021-07-09T20:01:57,083   creating build/temp.linux-armv7l-3.9/MDTraj/dcd
2021-07-09T20:01:57,084   creating build/temp.linux-armv7l-3.9/MDTraj/dcd/src
2021-07-09T20:01:57,084   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/dcd/include/ -IMDTraj/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/dcd/dcd.c -o build/temp.linux-armv7l-3.9/MDTraj/dcd/dcd.o
2021-07-09T20:01:57,478   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-09T20:01:57,479                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-09T20:01:57,479                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-09T20:01:57,479                    from MDTraj/dcd/dcd.c:314:
2021-07-09T20:01:57,479   /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]
2021-07-09T20:01:57,479      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-09T20:01:57,479         |  ^~~~~~~
2021-07-09T20:01:57,762   MDTraj/dcd/dcd.c: In function ‘__Pyx_ParseOptionalKeywords’:
2021-07-09T20:01:57,766   MDTraj/dcd/dcd.c:7916:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,766    7916 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,766         |                     ^
2021-07-09T20:01:57,767   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,767                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,767                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,767   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,767     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,767         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,771   MDTraj/dcd/dcd.c:7916:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,772    7916 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,772         |                     ^
2021-07-09T20:01:57,772   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,772                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,772                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,772   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:57,772     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:57,773         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,776   MDTraj/dcd/dcd.c:7916:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,776    7916 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,777         |                     ^
2021-07-09T20:01:57,777   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,777                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,777                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,777   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,777     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,777         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,781   MDTraj/dcd/dcd.c:7916:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,781    7916 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,781         |                     ^
2021-07-09T20:01:57,782   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,782                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,782                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,782   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,782     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,782         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,786   MDTraj/dcd/dcd.c:7916:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,786    7916 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,786         |                     ^
2021-07-09T20:01:57,786   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,786                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,787                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,787   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:57,787     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:57,787         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,791   MDTraj/dcd/dcd.c:7916:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,791    7916 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,791         |                     ^
2021-07-09T20:01:57,791   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,791                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,791                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,792   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,792     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,792         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,797   MDTraj/dcd/dcd.c:7932:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,797    7932 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,797         |                         ^
2021-07-09T20:01:57,797   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,797                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,797                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,797   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,798     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,798         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,801   MDTraj/dcd/dcd.c:7932:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,802    7932 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,802         |                         ^
2021-07-09T20:01:57,802   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,802                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,802                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,802   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:57,802     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:57,802         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,806   MDTraj/dcd/dcd.c:7932:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,806    7932 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,806         |                         ^
2021-07-09T20:01:57,807   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,807                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,807                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,807   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,807     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,807         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,811   MDTraj/dcd/dcd.c:7932:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,811    7932 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,811         |                         ^
2021-07-09T20:01:57,811   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,812                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,812                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,812   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,812     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,812         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,816   MDTraj/dcd/dcd.c:7932:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,816    7932 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,816         |                         ^
2021-07-09T20:01:57,816   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,816                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,816                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,816   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:57,817     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:57,817         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,820   MDTraj/dcd/dcd.c:7932:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,821    7932 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:01:57,821         |                         ^
2021-07-09T20:01:57,821   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,821                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,821                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,821   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,821     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,822         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,835   MDTraj/dcd/dcd.c: In function ‘__Pyx_Raise’:
2021-07-09T20:01:57,839   MDTraj/dcd/dcd.c:8121:9: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,840    8121 |         owned_instance = PyEval_CallObject(type, args);
2021-07-09T20:01:57,840         |         ^~~~~~~~~~~~~~
2021-07-09T20:01:57,840   In file included from /usr/include/python3.9/Python.h:145,
2021-07-09T20:01:57,840                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,840   /usr/include/python3.9/ceval.h:17:43: note: declared here
2021-07-09T20:01:57,840      17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
2021-07-09T20:01:57,840         |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,977   MDTraj/dcd/dcd.c: In function ‘__Pyx_PyObject_AsStringAndSize’:
2021-07-09T20:01:57,983   MDTraj/dcd/dcd.c:10339:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,983   10339 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:57,983         |             ^
2021-07-09T20:01:57,983   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,983                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,983                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,983   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,984     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,984         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,989   MDTraj/dcd/dcd.c:10339:13: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,990   10339 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:57,990         |             ^
2021-07-09T20:01:57,990   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,990                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,990                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,990   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:01:57,990     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:01:57,990         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:57,996   MDTraj/dcd/dcd.c:10339:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:01:57,996   10339 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:01:57,996         |             ^
2021-07-09T20:01:57,997   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:01:57,997                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:01:57,997                    from MDTraj/dcd/dcd.c:16:
2021-07-09T20:01:57,997   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:01:57,997     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:01:57,997         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:58,002   MDTraj/dcd/dcd.c:10340:20: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-09T20:01:58,002   10340 |             return PyUnicode_AsUTF8(o);
2021-07-09T20:01:58,002         |                    ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:01:58,082   In file included from MDTraj/dcd/include/dcdplugin.h:1,
2021-07-09T20:01:58,082                    from MDTraj/dcd/dcd.c:316:
2021-07-09T20:01:58,082   At top level:
2021-07-09T20:01:58,082   MDTraj/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
2021-07-09T20:01:58,082     473 | static int fio_write_str(fio_fd fd, const char *str) {
2021-07-09T20:01:58,083         |            ^~~~~~~~~~~~~
2021-07-09T20:01:58,083   MDTraj/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
2021-07-09T20:01:58,083     469 | static int fio_read_int32(fio_fd fd, int *i) {
2021-07-09T20:01:58,083         |            ^~~~~~~~~~~~~~
2021-07-09T20:01:58,083   MDTraj/dcd/include/fastio.h:465:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function]
2021-07-09T20:01:58,083     465 | static int fio_write_int32(fio_fd fd, int i) {
2021-07-09T20:01:58,083         |            ^~~~~~~~~~~~~~~
2021-07-09T20:01:58,083   MDTraj/dcd/include/fastio.h:456:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function]
2021-07-09T20:01:58,084     456 | static fio_size_t fio_ftell(fio_fd fd) {
2021-07-09T20:01:58,084         |                   ^~~~~~~~~
2021-07-09T20:01:58,084   MDTraj/dcd/include/fastio.h:449:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function]
2021-07-09T20:01:58,084     449 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {
2021-07-09T20:01:58,084         |                   ^~~~~~~~~
2021-07-09T20:01:58,084   MDTraj/dcd/include/fastio.h:414:19: warning: ‘fio_readv’ defined but not used [-Wunused-function]
2021-07-09T20:01:58,084     414 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {
2021-07-09T20:01:58,084         |                   ^~~~~~~~~
2021-07-09T20:01:58,085   MDTraj/dcd/include/fastio.h:393:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function]
2021-07-09T20:01:58,085     393 | static int fio_fclose(fio_fd fd) {
2021-07-09T20:01:58,085         |            ^~~~~~~~~~
2021-07-09T20:01:58,085   MDTraj/dcd/include/fastio.h:365:12: warning: ‘fio_open’ defined but not used [-Wunused-function]
2021-07-09T20:01:58,085     365 | static int fio_open(const char *filename, int mode, fio_fd *fd) {
2021-07-09T20:01:58,085         |            ^~~~~~~~
2021-07-09T20:02:03,756   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/dcd/include/ -IMDTraj/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-3.9/MDTraj/dcd/src/dcdplugin.o
2021-07-09T20:02:03,996   MDTraj/dcd/src/dcdplugin.c: In function ‘read_dcdheader’:
2021-07-09T20:02:03,997   MDTraj/dcd/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:02:03,997     129 |   } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
2021-07-09T20:02:03,997         |                                                         ^~
2021-07-09T20:02:03,998   MDTraj/dcd/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:02:03,998     146 |       if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) {
2021-07-09T20:02:03,998         |                                                      ^~
2021-07-09T20:02:03,999   MDTraj/dcd/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:02:03,999     164 |     if (input_integer[0] != dcdcordmagic) {
2021-07-09T20:02:03,999         |                          ^~
2021-07-09T20:02:04,003   MDTraj/dcd/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:02:04,003     341 |     if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
2021-07-09T20:02:04,003         |                                             ^~
2021-07-09T20:02:04,004   MDTraj/dcd/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T20:02:04,005     358 |     if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) {
2021-07-09T20:02:04,005         |                                             ^~
2021-07-09T20:02:04,009   MDTraj/dcd/src/dcdplugin.c: In function ‘read_dcdstep’:
2021-07-09T20:02:04,009   MDTraj/dcd/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:02:04,009     540 |         if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
2021-07-09T20:02:04,010         |                       ^~
2021-07-09T20:02:04,010   MDTraj/dcd/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-09T20:02:04,010     544 |           if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT;
2021-07-09T20:02:04,011         |                                           ^~
2021-07-09T20:02:04,035   In file included from MDTraj/dcd/src/dcdplugin.c:55:
2021-07-09T20:02:04,036   At top level:
2021-07-09T20:02:04,036   MDTraj/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]
2021-07-09T20:02:04,036      96 | static void swap2_aligned(void *v, long ndata) {
2021-07-09T20:02:04,037         |             ^~~~~~~~~~~~~
2021-07-09T20:02:04,037   MDTraj/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]
2021-07-09T20:02:04,037      32 | static void swap2_unaligned(void *v, long ndata) {
2021-07-09T20:02:04,037         |             ^~~~~~~~~~~~~~~
2021-07-09T20:02:04,037   In file included from MDTraj/dcd/src/dcdplugin.c:46:
2021-07-09T20:02:04,037   MDTraj/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
2021-07-09T20:02:04,038     473 | static int fio_write_str(fio_fd fd, const char *str) {
2021-07-09T20:02:04,038         |            ^~~~~~~~~~~~~
2021-07-09T20:02:04,038   MDTraj/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
2021-07-09T20:02:04,038     469 | static int fio_read_int32(fio_fd fd, int *i) {
2021-07-09T20:02:04,038         |            ^~~~~~~~~~~~~~
2021-07-09T20:02:05,194   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/dcd/dcd.o build/temp.linux-armv7l-3.9/MDTraj/dcd/src/dcdplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/dcd.cpython-39-arm-linux-gnueabihf.so
2021-07-09T20:02:05,334   building 'mdtraj.binpos' extension
2021-07-09T20:02:05,335   creating build/temp.linux-armv7l-3.9/MDTraj/binpos
2021-07-09T20:02:05,336   creating build/temp.linux-armv7l-3.9/MDTraj/binpos/src
2021-07-09T20:02:05,336   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/binpos/include/ -IMDTraj/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/binpos/binpos.c -o build/temp.linux-armv7l-3.9/MDTraj/binpos/binpos.o
2021-07-09T20:02:05,732   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-09T20:02:05,732                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-09T20:02:05,732                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-09T20:02:05,732                    from MDTraj/binpos/binpos.c:314:
2021-07-09T20:02:05,732   /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]
2021-07-09T20:02:05,733      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-09T20:02:05,733         |  ^~~~~~~
2021-07-09T20:02:05,890   MDTraj/binpos/binpos.c: In function ‘__Pyx_ParseOptionalKeywords’:
2021-07-09T20:02:05,893   MDTraj/binpos/binpos.c:6879:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,894    6879 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,894         |                     ^
2021-07-09T20:02:05,895   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,895                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,895                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,895   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:05,895     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:05,895         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,899   MDTraj/binpos/binpos.c:6879:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,900    6879 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,900         |                     ^
2021-07-09T20:02:05,900   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,900                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,900                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,900   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:02:05,901     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:02:05,901         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,905   MDTraj/binpos/binpos.c:6879:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,905    6879 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,905         |                     ^
2021-07-09T20:02:05,905   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,906                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,906                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,906   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:05,906     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:05,906         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,910   MDTraj/binpos/binpos.c:6879:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,910    6879 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,911         |                     ^
2021-07-09T20:02:05,911   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,911                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,911                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,911   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:05,911     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:05,911         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,915   MDTraj/binpos/binpos.c:6879:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,916    6879 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,916         |                     ^
2021-07-09T20:02:05,916   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,916                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,916                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,916   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:02:05,916     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:02:05,917         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,921   MDTraj/binpos/binpos.c:6879:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,921    6879 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,921         |                     ^
2021-07-09T20:02:05,921   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,921                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,922                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,922   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:05,922     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:05,922         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,926   MDTraj/binpos/binpos.c:6895:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,927    6895 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,927         |                         ^
2021-07-09T20:02:05,927   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,927                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,927                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,927   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:05,927     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:05,927         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,930   MDTraj/binpos/binpos.c:6895:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,930    6895 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,931         |                         ^
2021-07-09T20:02:05,931   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,931                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,931                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,931   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:02:05,931     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:02:05,931         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,934   MDTraj/binpos/binpos.c:6895:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,935    6895 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,935         |                         ^
2021-07-09T20:02:05,935   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,935                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,935                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,935   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:05,935     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:05,935         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,939   MDTraj/binpos/binpos.c:6895:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,939    6895 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,939         |                         ^
2021-07-09T20:02:05,939   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,939                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,940                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,940   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:05,940     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:05,940         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,944   MDTraj/binpos/binpos.c:6895:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,944    6895 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,944         |                         ^
2021-07-09T20:02:05,944   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,945                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,945                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,945   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:02:05,945     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:02:05,945         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,949   MDTraj/binpos/binpos.c:6895:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,949    6895 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
2021-07-09T20:02:05,949         |                         ^
2021-07-09T20:02:05,949   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:05,950                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:05,950                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,950   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:05,950     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:05,950         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:05,965   MDTraj/binpos/binpos.c: In function ‘__Pyx_Raise’:
2021-07-09T20:02:05,968   MDTraj/binpos/binpos.c:7101:9: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:05,968    7101 |         owned_instance = PyEval_CallObject(type, args);
2021-07-09T20:02:05,968         |         ^~~~~~~~~~~~~~
2021-07-09T20:02:05,969   In file included from /usr/include/python3.9/Python.h:145,
2021-07-09T20:02:05,969                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:05,969   /usr/include/python3.9/ceval.h:17:43: note: declared here
2021-07-09T20:02:05,969      17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
2021-07-09T20:02:05,969         |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:06,091   MDTraj/binpos/binpos.c: In function ‘__Pyx_PyObject_AsStringAndSize’:
2021-07-09T20:02:06,096   MDTraj/binpos/binpos.c:9306:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:06,096    9306 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:02:06,096         |             ^
2021-07-09T20:02:06,096   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:06,096                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:06,096                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:06,096   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:06,097     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:06,097         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:06,101   MDTraj/binpos/binpos.c:9306:13: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:06,102    9306 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:02:06,102         |             ^
2021-07-09T20:02:06,102   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:06,102                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:06,102                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:06,102   /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here
2021-07-09T20:02:06,102     580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
2021-07-09T20:02:06,103         |                                             ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:06,107   MDTraj/binpos/binpos.c:9306:13: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations]
2021-07-09T20:02:06,108    9306 |             *length = PyUnicode_GET_DATA_SIZE(o);
2021-07-09T20:02:06,108         |             ^
2021-07-09T20:02:06,108   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-09T20:02:06,108                    from /usr/include/python3.9/Python.h:97,
2021-07-09T20:02:06,108                    from MDTraj/binpos/binpos.c:16:
2021-07-09T20:02:06,108   /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here
2021-07-09T20:02:06,108     446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
2021-07-09T20:02:06,109         |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:06,113   MDTraj/binpos/binpos.c:9307:20: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2021-07-09T20:02:06,113    9307 |             return PyUnicode_AsUTF8(o);
2021-07-09T20:02:06,113         |                    ^~~~~~~~~~~~~~~~~~~
2021-07-09T20:02:08,192   MDTraj/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_6binpos_20BINPOSTrajectoryFile_7_read’:
2021-07-09T20:02:08,194   MDTraj/binpos/binpos.c:3114:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-09T20:02:08,194    3114 |   if (__pyx_t_2) {
2021-07-09T20:02:08,194         |      ^
2021-07-09T20:02:08,195   MDTraj/binpos/binpos.c:2631:7: note: ‘__pyx_v_status’ was declared here
2021-07-09T20:02:08,195    2631 |   int __pyx_v_status;
2021-07-09T20:02:08,195         |       ^~~~~~~~~~~~~~
2021-07-09T20:02:08,195   MDTraj/binpos/binpos.c:198:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-09T20:02:08,196     198 |   #define PyInt_FromSsize_t            PyLong_FromSsize_t
2021-07-09T20:02:08,196         |                                        ^~~~~~~~~~~~~~~~~~
2021-07-09T20:02:08,197   MDTraj/binpos/binpos.c:2628:7: note: ‘__pyx_v_i’ was declared here
2021-07-09T20:02:08,197    2628 |   int __pyx_v_i;
2021-07-09T20:02:08,197         |       ^~~~~~~~~
2021-07-09T20:02:11,019   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/binpos/include/ -IMDTraj/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/binpos/src/binposplugin.c -o build/temp.linux-armv7l-3.9/MDTraj/binpos/src/binposplugin.o
2021-07-09T20:02:11,151   MDTraj/binpos/src/binposplugin.c: In function ‘seek_timestep’:
2021-07-09T20:02:11,151   MDTraj/binpos/src/binposplugin.c:105:9: warning: unused variable ‘i’ [-Wunused-variable]
2021-07-09T20:02:11,151     105 |     int i, numatoms;
2021-07-09T20:02:11,152         |         ^
2021-07-09T20:02:11,152   MDTraj/binpos/src/binposplugin.c: In function ‘tell_timestep’:
2021-07-09T20:02:11,153   MDTraj/binpos/src/binposplugin.c:128:9: warning: unused variable ‘i’ [-Wunused-variable]
2021-07-09T20:02:11,153     128 |     int i, numatoms, frame;
2021-07-09T20:02:11,153         |         ^
2021-07-09T20:02:11,379   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/binpos/binpos.o build/temp.linux-armv7l-3.9/MDTraj/binpos/src/binposplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/binpos.cpython-39-arm-linux-gnueabihf.so
2021-07-09T20:02:11,516   building 'mdtraj._rmsd' extension
2021-07-09T20:02:11,516   creating build/temp.linux-armv7l-3.9/MDTraj/rmsd
2021-07-09T20:02:11,517   creating build/temp.linux-armv7l-3.9/MDTraj/rmsd/src
2021-07-09T20:02:11,518   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 -msse2 -O3 -funroll-loops -fopenmp
2021-07-09T20:02:11,533   arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’
2021-07-09T20:02:11,535   error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1
2021-07-09T20:02:11,655   Building wheel for mdtraj (setup.py): finished with status 'error'
2021-07-09T20:02:11,655   ERROR: Failed building wheel for mdtraj
2021-07-09T20:02:11,656   Running setup.py clean for mdtraj
2021-07-09T20:02:11,656   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-rm9cspv0/mdtraj_fb40759775e54c2984254970ca458555/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-rm9cspv0/mdtraj_fb40759775e54c2984254970ca458555/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
2021-07-09T20:02:13,142   Attempting to autodetect OpenMP support... Compiler supports OpenMP
2021-07-09T20:02:13,331   running clean
2021-07-09T20:02:13,333   removing 'build/temp.linux-armv7l-3.9' (and everything under it)
2021-07-09T20:02:13,345   removing 'build/lib.linux-armv7l-3.9' (and everything under it)
2021-07-09T20:02:13,393   'build/bdist.linux-armv7l' does not exist -- can't clean it
2021-07-09T20:02:13,393   'build/scripts-3.9' does not exist -- can't clean it
2021-07-09T20:02:13,393   removing 'build'
2021-07-09T20:02:13,500 Failed to build mdtraj
2021-07-09T20:02:13,501 ERROR: Failed to build one or more wheels
2021-07-09T20:02:13,501 Exception information:
2021-07-09T20:02:13,501 Traceback (most recent call last):
2021-07-09T20:02:13,501   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main
2021-07-09T20:02:13,501     status = self.run(options, args)
2021-07-09T20:02:13,501   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
2021-07-09T20:02:13,501     return func(self, options, args)
2021-07-09T20:02:13,501   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run
2021-07-09T20:02:13,501     raise CommandError(
2021-07-09T20:02:13,501 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2021-07-09T20:02:13,509 Removed build tracker: '/tmp/pip-req-tracker-jau_1hs0'