2021-07-14T22:06:22,954 Created temporary directory: /tmp/pip-ephem-wheel-cache-mvtcbn_o 2021-07-14T22:06:22,957 Created temporary directory: /tmp/pip-req-tracker-6k4v2ikl 2021-07-14T22:06:22,958 Initialized build tracking at /tmp/pip-req-tracker-6k4v2ikl 2021-07-14T22:06:22,958 Created build tracker: /tmp/pip-req-tracker-6k4v2ikl 2021-07-14T22:06:22,958 Entered build tracker: /tmp/pip-req-tracker-6k4v2ikl 2021-07-14T22:06:22,959 Created temporary directory: /tmp/pip-wheel-nc8gcyoh 2021-07-14T22:06:22,990 1 location(s) to search for versions of mdanalysis: 2021-07-14T22:06:22,990 * https://pypi.org/simple/mdanalysis/ 2021-07-14T22:06:22,991 Fetching project page and analyzing links: https://pypi.org/simple/mdanalysis/ 2021-07-14T22:06:22,991 Getting page https://pypi.org/simple/mdanalysis/ 2021-07-14T22:06:22,993 Found index url https://pypi.org/simple 2021-07-14T22:06:23,191 Found link https://files.pythonhosted.org/packages/97/94/fd5a74e25fba58cfb514dc39ef4717baa392057503d6c38897f886b2c0c6/MDAnalysis-0.7.6.tar.gz#sha256=4225660533926ce808ae425f22edc643db296274ac3b95d9feae4eec0b38ff24 (from https://pypi.org/simple/mdanalysis/), version: 0.7.6 2021-07-14T22:06:23,191 Found link https://files.pythonhosted.org/packages/9d/32/36e44fd1b946331bd72c7cc8806dd2b37f597a49ac7ccfe2a64ad91e59f7/MDAnalysis-0.8.0rc2.tar.gz#sha256=5e14ea8593b80d93a75e4445965f79fb245a7b581ebc8389b9360b9145e88f32 (from https://pypi.org/simple/mdanalysis/), version: 0.8.0rc2 2021-07-14T22:06:23,192 Found link https://files.pythonhosted.org/packages/d9/c4/27ff9dcd35aeef52f41f01a6eff0328eda8a5fa6dfa8097daa9ff70dcdf8/MDAnalysis-0.8.0rc4.tar.gz#sha256=881af3c86c796995d3c48f803227ff9ae7c3f0b8f5b86e382ea0e24feda222c6 (from https://pypi.org/simple/mdanalysis/), version: 0.8.0rc4 2021-07-14T22:06:23,192 Found link https://files.pythonhosted.org/packages/35/04/425a87220983514ef06f87cd98f54db0a84eed5bec9dfd4b27b6799ae99e/MDAnalysis-0.8.0.tar.gz#sha256=8ef4eb5e71c749bdf9ee5c8d5f0d93200f0999c3306c31812bf1a164a60e728f (from https://pypi.org/simple/mdanalysis/), version: 0.8.0 2021-07-14T22:06:23,192 Found link https://files.pythonhosted.org/packages/7d/39/0afea6f9c2cb10259479800c3b8496c59ecdab8019d5c0cf868729db4c91/MDAnalysis-0.8.1rc1.tar.gz#sha256=8026cc164a14044d57eab6976af0629c522d41cb412233b4d0c0d42d54c90664 (from https://pypi.org/simple/mdanalysis/), version: 0.8.1rc1 2021-07-14T22:06:23,193 Found link https://files.pythonhosted.org/packages/9b/45/5cfc731f70af562c860d5b79329980b8b380dd8e283847c950c1f7af8d4c/MDAnalysis-0.8.1.tar.gz#sha256=115c640433ef64b8e85abdc13b2d8754ce328fc7b597707c921ad1f8f8e6e364 (from https://pypi.org/simple/mdanalysis/), version: 0.8.1 2021-07-14T22:06:23,193 Found link https://files.pythonhosted.org/packages/b5/f0/a3d1acd3fedafd4b56f3cc8f880acb7f7f0f1c68c46121b4c180975435bb/MDAnalysis-0.9.0-dev.tar.gz#sha256=bff57b3363da5b2b8000a2ac7af6a942704f8f76d26fdef68b402f6869e40dbd (from https://pypi.org/simple/mdanalysis/), version: 0.9.0-dev 2021-07-14T22:06:23,194 Found link https://files.pythonhosted.org/packages/3b/1a/3bd08be00e453a29b6bcbb3320bb91619539eef69ab5ddef46e4b477b34d/MDAnalysis-0.9.0.tar.gz#sha256=0a02b28f1cdbecd45f02a916f196b92289b0979451288bec8589b1694b81952b (from https://pypi.org/simple/mdanalysis/), version: 0.9.0 2021-07-14T22:06:23,194 Found link https://files.pythonhosted.org/packages/e5/28/dcafeb58175edede7e4393d5ccfeafc77c3ca8eac6dd2f14d3919e9d4c0c/MDAnalysis-0.9.1.tar.gz#sha256=c0cc40fc6d8326d227f02af5315b768cf20ed3348af8104d488b6327368b944b (from https://pypi.org/simple/mdanalysis/), version: 0.9.1 2021-07-14T22:06:23,195 Found link https://files.pythonhosted.org/packages/4e/59/72545bc442ee0f6a45cafbd3b0e99add0aca51cbbbe3a882cc930f993306/MDAnalysis-0.9.2.tar.gz#sha256=2632e77bd30f6a088d59b599bb16269bf5c6ad02559e45fb630a08190c611800 (from https://pypi.org/simple/mdanalysis/), version: 0.9.2 2021-07-14T22:06:23,195 Found link https://files.pythonhosted.org/packages/82/db/8d468530d1a4834031166fcd9fb754a13e3fd5cc65ee09970ec57c9948cb/MDAnalysis-0.10.0.tar.gz#sha256=f0d1b79c75208ad40621aa8f9d999edb5129362d27c942fea11e4f14c9f4af72 (from https://pypi.org/simple/mdanalysis/), version: 0.10.0 2021-07-14T22:06:23,195 Found link https://files.pythonhosted.org/packages/18/80/e6a5502a43f2ce2c432e08a9b404febc46fd403fb5e4b13ddc429f676fd7/MDAnalysis-0.11.0.tar.gz#sha256=4ceff8a3d8bfc32b42d6500d04a3f0c75e186d6811505b78eea3dacb5c368bb0 (from https://pypi.org/simple/mdanalysis/), version: 0.11.0 2021-07-14T22:06:23,196 Found link https://files.pythonhosted.org/packages/66/77/d666034a559dc75a0cc485345f3058b45b8b067a858adb009b6fae0bcefc/MDAnalysis-0.12.1.tar.gz#sha256=a7d0f28cbc2fa566af664057360c0d7466aba719342fdfccfe8c46380466a4b5 (from https://pypi.org/simple/mdanalysis/), version: 0.12.1 2021-07-14T22:06:23,196 Found link https://files.pythonhosted.org/packages/78/33/704a708797267b35bfe27cc40e83eedabad62c7bb143babbc728ee285082/MDAnalysis-0.13.0.tar.gz#sha256=bdf5a15842bd4e4635fcb60297978252c55c5828c9b7003d810c9e19a4fffbe6 (from https://pypi.org/simple/mdanalysis/), version: 0.13.0 2021-07-14T22:06:23,197 Found link https://files.pythonhosted.org/packages/11/4c/1b683b1448f14e73f8a45981e27689ca694d5f1106e0453145f8619ffc0c/MDAnalysis-0.14.0.tar.gz#sha256=3006cc0479b63e31ce6681f4db1f4e94f786aef2ec431670bc10f715c6dfec05 (from https://pypi.org/simple/mdanalysis/), version: 0.14.0 2021-07-14T22:06:23,197 Found link https://files.pythonhosted.org/packages/9f/56/a4cae14e45aa893a3578905a97e17a325d663e424736366adbc134e72dce/MDAnalysis-0.15.0.tar.gz#sha256=9088786048b47339cba1f8a586977bbb3bb04ae1bcd0462b59e45bda37e25533 (from https://pypi.org/simple/mdanalysis/), version: 0.15.0 2021-07-14T22:06:23,198 Found link https://files.pythonhosted.org/packages/55/bb/32c3dbd8e92b661a98839a50bd3185d29949afe4618fc1a846e42bad0ebf/MDAnalysis-0.16.0.tar.gz#sha256=c4824fa1fddd336daa39371436187ebb023366885fb250c2827ed7fce2546bd4 (from https://pypi.org/simple/mdanalysis/), version: 0.16.0 2021-07-14T22:06:23,198 Found link https://files.pythonhosted.org/packages/5f/68/7e7ce717700411e25821100a3bc3d31866ef7abee7e282736f9e0635fef7/MDAnalysis-0.16.1.tar.gz#sha256=3dc8f5d639ab3a0d152cbd7259ae9372ec8a9bac0f8cb7d3b80ce5adc1e3ee57 (from https://pypi.org/simple/mdanalysis/), version: 0.16.1 2021-07-14T22:06:23,198 Found link https://files.pythonhosted.org/packages/ae/d5/07c38db64a6bd9bcec03caea8e07137bb2e571ce2bd145f9804727dfc2a5/MDAnalysis-0.16.2.tar.gz#sha256=407d9a9ff1ab8a5e47973714d06fabff220f8d08a28792dee93e88e70e995b0a (from https://pypi.org/simple/mdanalysis/), version: 0.16.2 2021-07-14T22:06:23,199 Found link https://files.pythonhosted.org/packages/91/e0/b12ee57016dffcf8da1f5651745ab981a09bc9e51519b6fa752a1a9a6d0f/MDAnalysis-0.17.0.tar.gz#sha256=9bd61760334698cc7b8a57ad26456451e926e9c9e66722594ad8816561348cde (from https://pypi.org/simple/mdanalysis/), version: 0.17.0 2021-07-14T22:06:23,199 Found link https://files.pythonhosted.org/packages/17/44/e9aff78fc88f6b8ac56b7626f3c83ed3c53f723b3f756d4c211ebd5add74/MDAnalysis-0.18.0.tar.gz#sha256=a08acea1755112411e7db55e3f282e164b47a59e15794b38744cce6c596f252a (from https://pypi.org/simple/mdanalysis/), version: 0.18.0 2021-07-14T22:06:23,200 Found link https://files.pythonhosted.org/packages/6e/30/a2b4339369e252bf22dc8d1e732870bf88c33a73e4f5e73788c1a65b25a3/MDAnalysis-0.19.0.tar.gz#sha256=248e3b37fc6150e31c609cc18a3927c32aee37b76d29cbfedf635e7e1aa982cf (from https://pypi.org/simple/mdanalysis/), version: 0.19.0 2021-07-14T22:06:23,200 Found link https://files.pythonhosted.org/packages/1c/24/b03a9bf48a1703b1ec31c34585aab123ca73e7778155ac3d5301a564fde6/MDAnalysis-0.19.1.tar.gz#sha256=ff1d694f8598c0833ec340de6a6adb3b5e62b92d0fa94ee6401718ba972db3cc (from https://pypi.org/simple/mdanalysis/), version: 0.19.1 2021-07-14T22:06:23,200 Found link https://files.pythonhosted.org/packages/be/72/6c2f9fcd842c9a50315ac93c4079b3f70735c6125fe903d04fb68a6e616a/MDAnalysis-0.19.2.tar.gz#sha256=c5395bbafa5efca2e1aee4715d26129844140c47cb8301da0293106cb969de7d (from https://pypi.org/simple/mdanalysis/), version: 0.19.2 2021-07-14T22:06:23,201 Found link https://files.pythonhosted.org/packages/b8/49/a0470dda3837aa4c42a7d2e69a4aaa1646ce2aeffe686f6887666f265b43/MDAnalysis-0.20.0.tar.gz#sha256=03938fc6c25bc16af7a2f5030118e6fb3d95b47a40ac70e887ba08048d87b33f (from https://pypi.org/simple/mdanalysis/), version: 0.20.0 2021-07-14T22:06:23,201 Found link https://files.pythonhosted.org/packages/83/4b/97c2df212f1eee47144648aa0e0da1a9022eab74d3fc1fbaf2767734de3d/MDAnalysis-0.20.1.tar.gz#sha256=d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9 (from https://pypi.org/simple/mdanalysis/), version: 0.20.1 2021-07-14T22:06:23,202 Found link https://files.pythonhosted.org/packages/c9/ae/11905971cc6cdb436bff040270f58fb3fc54ef77aea2ce2dfc269129f74e/MDAnalysis-1.0.0.tar.gz#sha256=f45a024aca45e390ff1c45ca90beb2180b78881be377e2a1aa9cd6c109bcfa81 (from https://pypi.org/simple/mdanalysis/), version: 1.0.0 2021-07-14T22:06:23,203 Link requires a different Python (3.9.2 not in: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9'): https://files.pythonhosted.org/packages/9e/19/1d32ded1891605facf6faf6e0de4ff6bd33db3f7983d84cfc10074363990/MDAnalysis-1.0.1.tar.gz#sha256=dc2cf34391b5eb1733fca1ab14e0de2e381d2d595c95923403f42cb2e39c9dad (from https://pypi.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2021-07-14T22:06:23,205 Link requires a different Python (3.9.2 not in: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9'): https://files.pythonhosted.org/packages/0f/5a/3f34615abbe7c7758847636167d0caad7bb428c3950da64e7a3003b2c6fc/MDAnalysis-1.1.0.tar.gz#sha256=17cafb982e4380d62c6e2ba951c7717e9393b4c7b6200b6632763100ea2b0839 (from https://pypi.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2021-07-14T22:06:23,207 Link requires a different Python (3.9.2 not in: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9'): https://files.pythonhosted.org/packages/43/64/5fc4d327f242130f983b9a1ded4a406191385370dbc55a7be99f8ead126d/MDAnalysis-1.1.1.tar.gz#sha256=edfd5a8ac6cbaa8d02f505ac3e68d5a1866644a2d392a8f20e279c43e0886253 (from https://pypi.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2021-07-14T22:06:23,207 Found link https://files.pythonhosted.org/packages/55/d1/9e302a51bdf6b3d0b7045c20b42203ad8ad20bf2103e8c19db2da868c6e7/MDAnalysis-2.0.0b0.tar.gz#sha256=09e0b855bddca9c386d3d674e3baf684ebcbb1668348844372232dc2b9a4ea4e (from https://pypi.org/simple/mdanalysis/), version: 2.0.0b0 2021-07-14T22:06:23,208 Skipping link: not a file: https://pypi.org/simple/mdanalysis/ 2021-07-14T22:06:23,230 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates 2021-07-14T22:06:23,250 Collecting mdanalysis==0.20.1 2021-07-14T22:06:23,252 Created temporary directory: /tmp/pip-unpack-6_j_si85 2021-07-14T22:06:24,569 Downloading MDAnalysis-0.20.1.tar.gz (3.7 MB) 2021-07-14T22:06:26,610 Added mdanalysis==0.20.1 from https://files.pythonhosted.org/packages/83/4b/97c2df212f1eee47144648aa0e0da1a9022eab74d3fc1fbaf2767734de3d/MDAnalysis-0.20.1.tar.gz#sha256=d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9 to build tracker '/tmp/pip-req-tracker-6k4v2ikl' 2021-07-14T22:06:26,612 Running setup.py (path:/tmp/pip-wheel-nc8gcyoh/mdanalysis_f42df4e0ff0e477198799d1297c8a85f/setup.py) egg_info for package mdanalysis 2021-07-14T22:06:26,612 Created temporary directory: /tmp/pip-pip-egg-info-0kjtayp9 2021-07-14T22:06:26,613 Running command python setup.py egg_info 2021-07-14T22:06:27,729 /tmp/pip-wheel-nc8gcyoh/mdanalysis_f42df4e0ff0e477198799d1297c8a85f/setup.py:126: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. 2021-07-14T22:06:27,730 self.config = configparser.SafeConfigParser() 2021-07-14T22:06:28,291 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-14T22:06:28,291 Will not attempt to use Cython. 2021-07-14T22:06:28,292 running egg_info 2021-07-14T22:06:28,293 creating /tmp/pip-pip-egg-info-0kjtayp9/MDAnalysis.egg-info 2021-07-14T22:06:28,294 writing /tmp/pip-pip-egg-info-0kjtayp9/MDAnalysis.egg-info/PKG-INFO 2021-07-14T22:06:28,297 writing dependency_links to /tmp/pip-pip-egg-info-0kjtayp9/MDAnalysis.egg-info/dependency_links.txt 2021-07-14T22:06:28,299 writing requirements to /tmp/pip-pip-egg-info-0kjtayp9/MDAnalysis.egg-info/requires.txt 2021-07-14T22:06:28,300 writing top-level names to /tmp/pip-pip-egg-info-0kjtayp9/MDAnalysis.egg-info/top_level.txt 2021-07-14T22:06:28,302 writing manifest file '/tmp/pip-pip-egg-info-0kjtayp9/MDAnalysis.egg-info/SOURCES.txt' 2021-07-14T22:06:28,507 reading manifest file '/tmp/pip-pip-egg-info-0kjtayp9/MDAnalysis.egg-info/SOURCES.txt' 2021-07-14T22:06:28,509 reading manifest template 'MANIFEST.in' 2021-07-14T22:06:28,587 warning: no files found matching 'MDAnalysis/coordinates/xdrfile/src/*' 2021-07-14T22:06:28,588 warning: no files found matching 'MDAnalysis/lib/src/pyqcprot/*' 2021-07-14T22:06:28,684 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-14T22:06:28,686 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2021-07-14T22:06:28,688 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2021-07-14T22:06:28,690 warning: no previously-included files matching '*~' found anywhere in distribution 2021-07-14T22:06:28,690 adding license file 'LICENSE' 2021-07-14T22:06:28,690 adding license file 'AUTHORS' 2021-07-14T22:06:28,707 writing manifest file '/tmp/pip-pip-egg-info-0kjtayp9/MDAnalysis.egg-info/SOURCES.txt' 2021-07-14T22:06:28,805 Source in /tmp/pip-wheel-nc8gcyoh/mdanalysis_f42df4e0ff0e477198799d1297c8a85f has version 0.20.1, which satisfies requirement mdanalysis==0.20.1 from https://files.pythonhosted.org/packages/83/4b/97c2df212f1eee47144648aa0e0da1a9022eab74d3fc1fbaf2767734de3d/MDAnalysis-0.20.1.tar.gz#sha256=d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9 2021-07-14T22:06:28,806 Removed mdanalysis==0.20.1 from https://files.pythonhosted.org/packages/83/4b/97c2df212f1eee47144648aa0e0da1a9022eab74d3fc1fbaf2767734de3d/MDAnalysis-0.20.1.tar.gz#sha256=d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9 from build tracker '/tmp/pip-req-tracker-6k4v2ikl' 2021-07-14T22:06:28,811 Created temporary directory: /tmp/pip-unpack-op2ni1h5 2021-07-14T22:06:28,812 Building wheels for collected packages: mdanalysis 2021-07-14T22:06:28,817 Created temporary directory: /tmp/pip-wheel-0pbp0cpp 2021-07-14T22:06:28,817 Building wheel for mdanalysis (setup.py): started 2021-07-14T22:06:28,818 Destination directory: /tmp/pip-wheel-0pbp0cpp 2021-07-14T22:06:28,818 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-nc8gcyoh/mdanalysis_f42df4e0ff0e477198799d1297c8a85f/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-nc8gcyoh/mdanalysis_f42df4e0ff0e477198799d1297c8a85f/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-0pbp0cpp 2021-07-14T22:06:29,942 /tmp/pip-wheel-nc8gcyoh/mdanalysis_f42df4e0ff0e477198799d1297c8a85f/setup.py:126: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. 2021-07-14T22:06:29,943 self.config = configparser.SafeConfigParser() 2021-07-14T22:06:30,195 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-14T22:06:30,195 Will not attempt to use Cython. 2021-07-14T22:06:30,486 running bdist_wheel 2021-07-14T22:06:30,489 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2021-07-14T22:06:30,492 running build 2021-07-14T22:06:30,492 running build_py 2021-07-14T22:06:30,638 creating build 2021-07-14T22:06:30,638 creating build/lib.linux-armv7l-3.9 2021-07-14T22:06:30,639 creating build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:30,640 copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:30,642 copying MDAnalysis/KDTree.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:30,644 copying MDAnalysis/version.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:30,646 copying MDAnalysis/due.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:30,648 copying MDAnalysis/authors.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:30,649 copying MDAnalysis/units.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:30,652 copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:30,656 creating build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,657 copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,659 copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,662 copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,664 copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,666 copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,669 copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,671 copying MDAnalysis/topology/_elements.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,673 copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,676 copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,678 copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,681 copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,684 copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,687 copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,689 copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,692 copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,694 copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,697 copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,700 copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,703 copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,705 copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,708 copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,710 copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,712 copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,715 copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,718 copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,721 copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-14T22:06:30,724 creating build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,725 copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,729 copying MDAnalysis/core/AtomGroup.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,731 copying MDAnalysis/core/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,733 copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,736 copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,741 copying MDAnalysis/core/transformations.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,743 copying MDAnalysis/core/units.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,745 copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,752 copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,756 copying MDAnalysis/core/qcprot.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,758 copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,761 copying MDAnalysis/core/log.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,763 copying MDAnalysis/core/util.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,766 copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,769 copying MDAnalysis/core/parallel.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,772 copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-14T22:06:30,777 creating build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,778 copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,783 copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,786 copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,789 copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,794 copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,797 copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,799 copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,802 copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:30,807 creating build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-14T22:06:30,809 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-14T22:06:30,812 copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-14T22:06:30,816 copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-14T22:06:30,821 creating build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,822 copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,825 copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,830 copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,833 copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,836 copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,839 copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,842 copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,846 copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,850 copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,855 copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,857 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,860 copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,863 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,866 copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,869 copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,872 copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,875 copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,878 copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,882 copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,884 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,888 copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,891 copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,895 copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,897 copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,901 copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,904 copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,907 copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-14T22:06:30,912 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,914 copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,917 copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,921 copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,924 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,927 copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,931 copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,934 copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,937 copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,941 copying MDAnalysis/analysis/helanal.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,945 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,948 copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,951 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,954 copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,959 copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,962 copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,966 copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,969 copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,972 copying MDAnalysis/analysis/x3dna.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,975 copying MDAnalysis/analysis/hole.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,980 copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,984 copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:06:30,988 creating build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-14T22:06:30,990 copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-14T22:06:30,993 copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-14T22:06:30,996 copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-14T22:06:30,999 copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-14T22:06:31,002 copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-14T22:06:31,006 creating build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-14T22:06:31,007 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-14T22:06:31,010 copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-14T22:06:31,012 copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-14T22:06:31,015 copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-14T22:06:31,018 copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-14T22:06:31,020 copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-14T22:06:31,023 copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-14T22:06:31,026 creating build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-14T22:06:31,028 copying MDAnalysis/migration/ten2eleven.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-14T22:06:31,030 copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-14T22:06:31,033 copying MDAnalysis/migration/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-14T22:06:31,035 copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-14T22:06:31,041 creating build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-14T22:06:31,043 copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-14T22:06:31,047 copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-14T22:06:31,050 copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-14T22:06:31,054 copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-14T22:06:31,058 creating build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-14T22:06:31,059 copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-14T22:06:31,062 copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-14T22:06:31,066 creating build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-14T22:06:31,068 copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-14T22:06:31,071 copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-14T22:06:31,074 copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-14T22:06:31,078 copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-14T22:06:31,082 creating build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats 2021-07-14T22:06:31,083 copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats 2021-07-14T22:06:31,087 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy 2021-07-14T22:06:31,088 copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy 2021-07-14T22:06:31,091 copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy 2021-07-14T22:06:31,096 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-14T22:06:31,097 copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-14T22:06:31,102 copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-14T22:06:31,107 copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-14T22:06:31,112 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-14T22:06:31,116 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-14T22:06:31,117 copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-14T22:06:31,120 copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-14T22:06:31,123 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-14T22:06:31,125 copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-14T22:06:31,129 copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-14T22:06:31,134 copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-14T22:06:31,142 copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-14T22:06:31,145 copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-14T22:06:31,147 copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-14T22:06:31,152 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-14T22:06:31,154 copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-14T22:06:31,158 copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-14T22:06:31,161 copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-14T22:06:31,165 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-14T22:06:31,170 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:06:31,171 copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:06:31,175 copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:06:31,178 copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:06:31,182 creating build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,183 copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,186 copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,189 copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,192 copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,194 copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,197 copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,199 copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,202 copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,205 copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,207 copying MDAnalysis/migration/fixes/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,209 copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,212 copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,215 copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,217 copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,220 copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-14T22:06:31,225 copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-14T22:06:31,230 copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-14T22:06:31,253 running build_ext 2021-07-14T22:06:31,257 building 'MDAnalysis.lib.formats.libdcd' extension 2021-07-14T22:06:31,553 creating build/temp.linux-armv7l-3.9 2021-07-14T22:06:31,554 creating build/temp.linux-armv7l-3.9/MDAnalysis 2021-07-14T22:06:31,555 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib 2021-07-14T22:06:31,556 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats 2021-07-14T22:06:31,557 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:06:32,091 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:06:32,091 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:06:32,091 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:06:32,091 from MDAnalysis/lib/formats/libdcd.c:627: 2021-07-14T22:06:32,091 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:06:32,092 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:06:32,092 | ^~~~~~~ 2021-07-14T22:06:32,162 In file included from MDAnalysis/lib/formats/libdcd.c:633: 2021-07-14T22:06:32,163 MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’: 2021-07-14T22:06:32,163 MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T22:06:32,163 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-14T22:06:32,163 | ^~ 2021-07-14T22:06:32,166 MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’: 2021-07-14T22:06:32,166 MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable] 2021-07-14T22:06:32,167 698 | struct tm *tmbuf; 2021-07-14T22:06:32,167 | ^~~~~ 2021-07-14T22:06:32,167 MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable] 2021-07-14T22:06:32,167 697 | time_t cur_time; 2021-07-14T22:06:32,168 | ^~~~~~~~ 2021-07-14T22:06:32,850 MDAnalysis/lib/formats/libdcd.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:06:32,864 MDAnalysis/lib/formats/libdcd.c:28948:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:32,864 28948 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:32,864 | ^ 2021-07-14T22:06:32,865 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:32,865 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:32,865 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:32,865 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:06:32,865 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:06:32,865 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:32,882 MDAnalysis/lib/formats/libdcd.c:28948:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:32,882 28948 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:32,882 | ^ 2021-07-14T22:06:32,882 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:32,883 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:32,883 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:32,883 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:06:32,883 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:06:32,883 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:32,899 MDAnalysis/lib/formats/libdcd.c:28948:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:32,899 28948 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:32,899 | ^ 2021-07-14T22:06:32,900 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:32,900 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:32,900 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:32,900 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:06:32,900 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:06:32,900 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:32,916 MDAnalysis/lib/formats/libdcd.c:28948:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:32,917 28948 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:32,917 | ^ 2021-07-14T22:06:32,917 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:32,917 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:32,917 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:32,917 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:06:32,918 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:06:32,918 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:32,934 MDAnalysis/lib/formats/libdcd.c:28948:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:32,934 28948 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:32,934 | ^ 2021-07-14T22:06:32,934 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:32,934 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:32,935 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:32,935 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:06:32,935 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:06:32,935 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:32,951 MDAnalysis/lib/formats/libdcd.c:28948:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:32,951 28948 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:32,951 | ^ 2021-07-14T22:06:32,952 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:32,952 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:32,952 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:32,952 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:06:32,952 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:06:32,952 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:32,972 MDAnalysis/lib/formats/libdcd.c:28964:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:32,972 28964 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:32,972 | ^ 2021-07-14T22:06:32,972 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:32,973 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:32,973 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:32,973 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:06:32,973 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:06:32,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:32,989 MDAnalysis/lib/formats/libdcd.c:28964:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:32,990 28964 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:32,990 | ^ 2021-07-14T22:06:32,990 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:32,990 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:32,990 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:32,991 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:06:32,991 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:06:32,991 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:33,007 MDAnalysis/lib/formats/libdcd.c:28964:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:33,007 28964 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:33,007 | ^ 2021-07-14T22:06:33,008 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:33,008 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:33,008 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:33,008 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:06:33,008 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:06:33,008 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:33,025 MDAnalysis/lib/formats/libdcd.c:28964:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:33,025 28964 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:33,025 | ^ 2021-07-14T22:06:33,025 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:33,025 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:33,026 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:33,026 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:06:33,026 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:06:33,026 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:33,042 MDAnalysis/lib/formats/libdcd.c:28964:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:33,042 28964 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:33,043 | ^ 2021-07-14T22:06:33,043 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:33,043 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:33,043 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:33,043 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:06:33,043 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:06:33,044 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:33,060 MDAnalysis/lib/formats/libdcd.c:28964:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:33,060 28964 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:06:33,060 | ^ 2021-07-14T22:06:33,061 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:33,061 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:33,061 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:33,061 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:06:33,061 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:06:33,061 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:33,489 MDAnalysis/lib/formats/libdcd.c: In function ‘__Pyx_decode_c_string’: 2021-07-14T22:06:33,504 MDAnalysis/lib/formats/libdcd.c:31209:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:06:33,505 31209 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-14T22:06:33,505 | ^~~~~~ 2021-07-14T22:06:33,505 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:06:33,505 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:06:33,506 from MDAnalysis/lib/formats/libdcd.c:33: 2021-07-14T22:06:33,506 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-14T22:06:33,506 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-14T22:06:33,506 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:06:34,406 In file included from MDAnalysis/lib/formats/include/readdcd.h:25, 2021-07-14T22:06:34,406 from MDAnalysis/lib/formats/libdcd.c:633: 2021-07-14T22:06:34,406 At top level: 2021-07-14T22:06:34,406 MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2021-07-14T22:06:34,407 96 | static void swap2_aligned(void *v, long ndata) { 2021-07-14T22:06:34,407 | ^~~~~~~~~~~~~ 2021-07-14T22:06:34,407 MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2021-07-14T22:06:34,408 32 | static void swap2_unaligned(void *v, long ndata) { 2021-07-14T22:06:34,408 | ^~~~~~~~~~~~~~~ 2021-07-14T22:06:34,408 In file included from MDAnalysis/lib/formats/libdcd.c:632: 2021-07-14T22:06:34,408 MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-14T22:06:34,408 453 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-14T22:06:34,409 | ^~~~~~~~~~~~~ 2021-07-14T22:06:34,409 MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-14T22:06:34,409 449 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-14T22:06:34,409 | ^~~~~~~~~~~~~~ 2021-07-14T22:07:15,425 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/MDAnalysis/lib/formats/libdcd.o -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:07:15,663 building 'MDAnalysis.lib.c_distances' extension 2021-07-14T22:07:15,664 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:07:16,145 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:07:16,146 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:07:16,146 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:07:16,146 from MDAnalysis/lib/c_distances.c:628: 2021-07-14T22:07:16,146 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:07:16,146 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:07:16,147 | ^~~~~~~ 2021-07-14T22:07:16,828 MDAnalysis/lib/c_distances.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:07:16,841 MDAnalysis/lib/c_distances.c:23529:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,841 23529 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,842 | ^ 2021-07-14T22:07:16,842 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,842 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,842 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,842 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:16,843 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:16,843 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,858 MDAnalysis/lib/c_distances.c:23529:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,859 23529 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,859 | ^ 2021-07-14T22:07:16,859 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,859 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,859 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,860 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:16,860 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:16,860 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,875 MDAnalysis/lib/c_distances.c:23529:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,875 23529 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,876 | ^ 2021-07-14T22:07:16,876 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,876 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,876 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,876 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:16,876 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:16,877 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,892 MDAnalysis/lib/c_distances.c:23529:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,892 23529 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,892 | ^ 2021-07-14T22:07:16,893 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,893 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,893 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,893 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:16,893 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:16,893 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,908 MDAnalysis/lib/c_distances.c:23529:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,909 23529 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,909 | ^ 2021-07-14T22:07:16,909 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,909 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,909 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,910 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:16,910 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:16,910 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,925 MDAnalysis/lib/c_distances.c:23529:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,925 23529 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,926 | ^ 2021-07-14T22:07:16,926 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,926 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,926 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,926 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:16,927 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:16,927 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,945 MDAnalysis/lib/c_distances.c:23545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,945 23545 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,945 | ^ 2021-07-14T22:07:16,946 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,946 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,946 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,946 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:16,946 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:16,946 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,961 MDAnalysis/lib/c_distances.c:23545:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,962 23545 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,962 | ^ 2021-07-14T22:07:16,962 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,962 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,962 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,963 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:16,963 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:16,963 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,978 MDAnalysis/lib/c_distances.c:23545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,978 23545 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,979 | ^ 2021-07-14T22:07:16,979 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,979 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,979 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,979 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:16,979 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:16,979 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:16,995 MDAnalysis/lib/c_distances.c:23545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:16,995 23545 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:16,995 | ^ 2021-07-14T22:07:16,995 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:16,996 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:16,996 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:16,996 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:16,996 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:16,996 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:17,011 MDAnalysis/lib/c_distances.c:23545:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:17,012 23545 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:17,012 | ^ 2021-07-14T22:07:17,012 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:17,012 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:17,012 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:17,013 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:17,013 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:17,013 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:17,028 MDAnalysis/lib/c_distances.c:23545:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:17,029 23545 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:17,029 | ^ 2021-07-14T22:07:17,029 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:17,029 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:17,029 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:17,029 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:17,030 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:17,030 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:17,275 MDAnalysis/lib/c_distances.c: In function ‘__Pyx_decode_c_string’: 2021-07-14T22:07:17,289 MDAnalysis/lib/c_distances.c:24772:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:17,289 24772 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-14T22:07:17,290 | ^~~~~~ 2021-07-14T22:07:17,290 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:17,290 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:17,290 from MDAnalysis/lib/c_distances.c:34: 2021-07-14T22:07:17,290 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-14T22:07:17,290 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-14T22:07:17,290 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:44,130 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/MDAnalysis/lib/c_distances.o -lm -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:07:44,338 building 'MDAnalysis.lib.c_distances_openmp' extension 2021-07-14T22:07:44,338 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 -DPARALLEL -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:07:44,768 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:07:44,768 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:07:44,768 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:07:44,768 from MDAnalysis/lib/c_distances_openmp.c:639: 2021-07-14T22:07:44,768 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:07:44,769 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:07:44,769 | ^~~~~~~ 2021-07-14T22:07:44,990 MDAnalysis/lib/c_distances_openmp.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:07:44,993 MDAnalysis/lib/c_distances_openmp.c:7760:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:44,994 7760 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:44,994 | ^ 2021-07-14T22:07:44,994 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:44,994 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:44,994 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:44,994 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:44,994 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:44,995 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:44,999 MDAnalysis/lib/c_distances_openmp.c:7760:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:44,999 7760 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:44,999 | ^ 2021-07-14T22:07:44,999 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:44,999 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:44,999 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:44,999 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:45,000 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:45,000 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,003 MDAnalysis/lib/c_distances_openmp.c:7760:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,003 7760 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,004 | ^ 2021-07-14T22:07:45,004 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,004 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,004 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,004 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:45,004 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:45,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,008 MDAnalysis/lib/c_distances_openmp.c:7760:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,008 7760 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,008 | ^ 2021-07-14T22:07:45,009 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,009 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,009 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,009 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:45,009 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:45,009 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,013 MDAnalysis/lib/c_distances_openmp.c:7760:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,013 7760 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,013 | ^ 2021-07-14T22:07:45,013 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,013 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,013 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,014 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:45,014 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:45,014 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,017 MDAnalysis/lib/c_distances_openmp.c:7760:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,018 7760 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,018 | ^ 2021-07-14T22:07:45,018 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,018 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,018 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,018 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:45,018 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:45,018 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,023 MDAnalysis/lib/c_distances_openmp.c:7776:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,024 7776 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,024 | ^ 2021-07-14T22:07:45,024 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,024 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,024 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,024 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:45,024 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:45,024 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,028 MDAnalysis/lib/c_distances_openmp.c:7776:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,028 7776 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,028 | ^ 2021-07-14T22:07:45,028 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,029 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,029 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,029 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:45,029 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:45,029 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,033 MDAnalysis/lib/c_distances_openmp.c:7776:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,033 7776 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,033 | ^ 2021-07-14T22:07:45,033 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,033 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,033 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,033 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:45,034 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:45,034 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,037 MDAnalysis/lib/c_distances_openmp.c:7776:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,038 7776 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,038 | ^ 2021-07-14T22:07:45,038 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,038 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,038 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,038 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:45,038 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:45,039 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,042 MDAnalysis/lib/c_distances_openmp.c:7776:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,042 7776 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,042 | ^ 2021-07-14T22:07:45,043 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,043 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,043 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,043 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:45,043 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:45,043 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:45,047 MDAnalysis/lib/c_distances_openmp.c:7776:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:45,047 7776 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:45,047 | ^ 2021-07-14T22:07:45,047 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:45,047 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:45,048 from MDAnalysis/lib/c_distances_openmp.c:45: 2021-07-14T22:07:45,048 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:45,048 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:45,048 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,087 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/MDAnalysis/lib/c_distances_openmp.o -lm -lgomp -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -fopenmp 2021-07-14T22:07:51,295 building 'MDAnalysis.lib.qcprot' extension 2021-07-14T22:07:51,296 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:07:51,726 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:07:51,726 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:07:51,727 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:07:51,727 from MDAnalysis/lib/qcprot.c:592: 2021-07-14T22:07:51,727 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:07:51,727 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:07:51,727 | ^~~~~~~ 2021-07-14T22:07:51,787 MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’: 2021-07-14T22:07:51,788 MDAnalysis/lib/qcprot.c:2204:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:07:51,788 2204 | for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) { 2021-07-14T22:07:51,789 | ^ 2021-07-14T22:07:51,792 MDAnalysis/lib/qcprot.c:2412:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:07:51,793 2412 | for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) { 2021-07-14T22:07:51,793 | ^ 2021-07-14T22:07:51,942 MDAnalysis/lib/qcprot.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:07:51,947 MDAnalysis/lib/qcprot.c:8432:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,947 8432 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,947 | ^ 2021-07-14T22:07:51,948 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,948 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,948 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,948 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:51,949 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:51,949 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,954 MDAnalysis/lib/qcprot.c:8432:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,954 8432 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,954 | ^ 2021-07-14T22:07:51,955 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,955 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,955 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,955 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:51,955 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:51,956 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,960 MDAnalysis/lib/qcprot.c:8432:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,960 8432 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,960 | ^ 2021-07-14T22:07:51,960 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,960 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,961 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,961 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:51,961 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:51,961 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,965 MDAnalysis/lib/qcprot.c:8432:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,965 8432 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,965 | ^ 2021-07-14T22:07:51,965 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,965 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,966 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,966 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:51,966 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:51,966 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,970 MDAnalysis/lib/qcprot.c:8432:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,970 8432 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,970 | ^ 2021-07-14T22:07:51,970 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,970 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,971 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,971 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:51,971 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:51,971 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,975 MDAnalysis/lib/qcprot.c:8432:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,975 8432 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,975 | ^ 2021-07-14T22:07:51,976 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,976 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,976 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,976 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:51,976 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:51,976 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,982 MDAnalysis/lib/qcprot.c:8448:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,982 8448 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,982 | ^ 2021-07-14T22:07:51,982 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,982 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,983 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,983 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:51,983 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:51,983 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,987 MDAnalysis/lib/qcprot.c:8448:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,987 8448 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,987 | ^ 2021-07-14T22:07:51,988 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,988 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,988 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,988 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:51,988 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:51,989 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,993 MDAnalysis/lib/qcprot.c:8448:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,993 8448 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,993 | ^ 2021-07-14T22:07:51,993 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,993 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,994 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,994 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:51,994 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:51,994 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:51,998 MDAnalysis/lib/qcprot.c:8448:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:51,998 8448 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:51,998 | ^ 2021-07-14T22:07:51,999 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:51,999 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:51,999 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:51,999 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:51,999 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:51,999 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:52,003 MDAnalysis/lib/qcprot.c:8448:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:52,003 8448 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:52,003 | ^ 2021-07-14T22:07:52,004 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:52,004 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:52,004 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:52,004 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:07:52,004 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:07:52,004 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:52,008 MDAnalysis/lib/qcprot.c:8448:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:52,008 8448 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:07:52,009 | ^ 2021-07-14T22:07:52,009 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:07:52,009 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:52,009 from MDAnalysis/lib/qcprot.c:29: 2021-07-14T22:07:52,009 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:07:52,009 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:07:52,010 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:57,716 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/MDAnalysis/lib/qcprot.o -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:07:57,859 building 'MDAnalysis.lib._transformations' extension 2021-07-14T22:07:57,860 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/src 2021-07-14T22:07:57,860 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/src/transformations 2021-07-14T22:07:57,861 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:07:58,264 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:07:58,264 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:07:58,265 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:07:58,265 from MDAnalysis/lib/src/transformations/transformations.c:73: 2021-07-14T22:07:58,265 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:07:58,265 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:07:58,265 | ^~~~~~~ 2021-07-14T22:07:58,338 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: 2021-07-14T22:07:58,339 MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,339 1845 | #pragma vector always 2021-07-14T22:07:58,339 | 2021-07-14T22:07:58,343 MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,343 1962 | #pragma vector always 2021-07-14T22:07:58,343 | 2021-07-14T22:07:58,343 MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,344 1986 | #pragma vector always 2021-07-14T22:07:58,344 | 2021-07-14T22:07:58,348 MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: 2021-07-14T22:07:58,349 MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:07:58,349 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { 2021-07-14T22:07:58,349 | ^~ 2021-07-14T22:07:58,349 In file included from /usr/include/python3.9/Python.h:97, 2021-07-14T22:07:58,350 from MDAnalysis/lib/src/transformations/transformations.c:68: 2021-07-14T22:07:58,350 /usr/include/python3.9/unicodeobject.h:177:43: note: declared here 2021-07-14T22:07:58,350 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( 2021-07-14T22:07:58,350 | ^~~~~~~~~~~~~~~~~ 2021-07-14T22:07:58,388 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: 2021-07-14T22:07:58,389 MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,389 3427 | #pragma vector always 2021-07-14T22:07:58,389 | 2021-07-14T22:07:58,392 MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,392 3508 | #pragma vector always 2021-07-14T22:07:58,392 | 2021-07-14T22:07:58,397 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: 2021-07-14T22:07:58,398 MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,398 3610 | #pragma vector always 2021-07-14T22:07:58,398 | 2021-07-14T22:07:58,398 MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,399 3615 | #pragma vector always 2021-07-14T22:07:58,399 | 2021-07-14T22:07:58,404 MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,404 3679 | #pragma vector always 2021-07-14T22:07:58,404 | 2021-07-14T22:07:58,404 MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-14T22:07:58,405 3684 | #pragma vector always 2021-07-14T22:07:58,405 | 2021-07-14T22:07:58,482 At top level: 2021-07-14T22:07:58,482 MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] 2021-07-14T22:07:58,482 910 | PyConverter_DoubleVector4Copy( 2021-07-14T22:07:58,482 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:58,483 MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] 2021-07-14T22:07:58,483 804 | PyConverter_DoubleArrayOrNone( 2021-07-14T22:07:58,483 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:07:58,483 MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] 2021-07-14T22:07:58,483 774 | PyConverter_DoubleArray( 2021-07-14T22:07:58,484 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:04,853 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/MDAnalysis/lib/src/transformations/transformations.o -lm -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:08:04,992 building 'MDAnalysis.lib.formats.libmdaxdr' extension 2021-07-14T22:08:04,993 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src 2021-07-14T22:08:04,994 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:08:05,402 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:08:05,402 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:08:05,403 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:08:05,403 from MDAnalysis/lib/formats/libmdaxdr.c:649: 2021-07-14T22:08:05,403 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:08:05,403 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:08:05,403 | ^~~~~~~ 2021-07-14T22:08:05,440 In file included from MDAnalysis/lib/formats/libmdaxdr.c:652: 2021-07-14T22:08:05,440 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:05,441 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:05,441 | 2021-07-14T22:08:05,443 In file included from MDAnalysis/lib/formats/libmdaxdr.c:653: 2021-07-14T22:08:05,443 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:05,443 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:05,443 | 2021-07-14T22:08:05,444 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2021-07-14T22:08:05,444 from MDAnalysis/lib/formats/libmdaxdr.c:653: 2021-07-14T22:08:05,444 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:05,445 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:05,445 | 2021-07-14T22:08:05,446 In file included from MDAnalysis/lib/formats/libmdaxdr.c:654: 2021-07-14T22:08:05,447 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:05,447 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:05,447 | 2021-07-14T22:08:06,090 MDAnalysis/lib/formats/libmdaxdr.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:08:06,104 MDAnalysis/lib/formats/libmdaxdr.c:28080:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,105 28080 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,105 | ^ 2021-07-14T22:08:06,106 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,106 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,106 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,106 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:06,106 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:06,106 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,123 MDAnalysis/lib/formats/libmdaxdr.c:28080:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,124 28080 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,124 | ^ 2021-07-14T22:08:06,124 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,124 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,124 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,125 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:08:06,125 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:08:06,125 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,142 MDAnalysis/lib/formats/libmdaxdr.c:28080:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,142 28080 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,142 | ^ 2021-07-14T22:08:06,143 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,143 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,143 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,143 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:06,143 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:06,143 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,160 MDAnalysis/lib/formats/libmdaxdr.c:28080:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,161 28080 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,161 | ^ 2021-07-14T22:08:06,161 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,161 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,161 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,161 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:06,162 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:06,162 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,179 MDAnalysis/lib/formats/libmdaxdr.c:28080:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,179 28080 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,179 | ^ 2021-07-14T22:08:06,180 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,180 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,180 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,180 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:08:06,180 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:08:06,180 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,197 MDAnalysis/lib/formats/libmdaxdr.c:28080:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,197 28080 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,198 | ^ 2021-07-14T22:08:06,198 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,198 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,198 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,198 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:06,199 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:06,199 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,219 MDAnalysis/lib/formats/libmdaxdr.c:28096:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,219 28096 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,219 | ^ 2021-07-14T22:08:06,220 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,220 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,220 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,220 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:06,220 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:06,220 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,237 MDAnalysis/lib/formats/libmdaxdr.c:28096:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,238 28096 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,238 | ^ 2021-07-14T22:08:06,238 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,238 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,238 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,239 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:08:06,239 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:08:06,239 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,256 MDAnalysis/lib/formats/libmdaxdr.c:28096:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,256 28096 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,256 | ^ 2021-07-14T22:08:06,257 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,257 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,257 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,257 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:06,257 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:06,257 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,274 MDAnalysis/lib/formats/libmdaxdr.c:28096:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,275 28096 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,275 | ^ 2021-07-14T22:08:06,275 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,275 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,275 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,275 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:06,276 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:06,276 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,293 MDAnalysis/lib/formats/libmdaxdr.c:28096:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,293 28096 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,293 | ^ 2021-07-14T22:08:06,294 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,294 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,294 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,294 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:08:06,294 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:08:06,294 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,312 MDAnalysis/lib/formats/libmdaxdr.c:28096:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,312 28096 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:06,313 | ^ 2021-07-14T22:08:06,313 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,313 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,313 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,313 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:06,313 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:06,314 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:06,572 MDAnalysis/lib/formats/libmdaxdr.c: In function ‘__Pyx_decode_c_string’: 2021-07-14T22:08:06,586 MDAnalysis/lib/formats/libmdaxdr.c:29610:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:06,586 29610 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-14T22:08:06,587 | ^~~~~~ 2021-07-14T22:08:06,587 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:06,587 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:06,587 from MDAnalysis/lib/formats/libmdaxdr.c:55: 2021-07-14T22:08:06,587 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-14T22:08:06,588 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-14T22:08:06,588 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:43,476 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:08:43,575 In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: 2021-07-14T22:08:43,575 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:43,575 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:43,576 | 2021-07-14T22:08:43,580 In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: 2021-07-14T22:08:43,580 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:43,581 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:43,581 | 2021-07-14T22:08:43,581 In file included from MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2021-07-14T22:08:43,581 from MDAnalysis/lib/formats/src/trr_seek.c:31: 2021-07-14T22:08:43,581 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:43,581 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:43,581 | 2021-07-14T22:08:43,583 MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’: 2021-07-14T22:08:43,584 MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable] 2021-07-14T22:08:43,585 39 | int result, framebytes, totalframebytes; 2021-07-14T22:08:43,585 | ^~~~~~~~~~~~~~~ 2021-07-14T22:08:43,586 MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable] 2021-07-14T22:08:43,586 38 | float time, lambda; 2021-07-14T22:08:43,586 | ^~~~~~ 2021-07-14T22:08:43,586 MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable] 2021-07-14T22:08:43,586 38 | float time, lambda; 2021-07-14T22:08:43,587 | ^~~~ 2021-07-14T22:08:43,702 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:08:43,848 In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: 2021-07-14T22:08:43,848 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:43,848 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:43,848 | 2021-07-14T22:08:43,859 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’: 2021-07-14T22:08:43,860 MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T22:08:43,860 501 | while (size >= num && num_of_bits < 32) 2021-07-14T22:08:43,860 | ^~ 2021-07-14T22:08:43,861 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’: 2021-07-14T22:08:43,861 MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:08:43,861 547 | while (bytes[num_of_bytes] >= num) 2021-07-14T22:08:43,861 | ^~ 2021-07-14T22:08:43,862 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’: 2021-07-14T22:08:43,862 MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T22:08:43,862 656 | if (num_of_bits >= num_of_bytes * 8) 2021-07-14T22:08:43,863 | ^~ 2021-07-14T22:08:43,863 MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T22:08:43,863 658 | for (i = 0; i < num_of_bytes; i++) 2021-07-14T22:08:43,863 | ^ 2021-07-14T22:08:43,863 MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T22:08:43,864 666 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-14T22:08:43,864 | ^ 2021-07-14T22:08:43,864 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’: 2021-07-14T22:08:43,864 MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:08:43,865 706 | if (lastbits < num_of_bits) 2021-07-14T22:08:43,865 | ^ 2021-07-14T22:08:43,866 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-14T22:08:43,866 MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:08:43,866 816 | if(size3>xfp->buf1size) 2021-07-14T22:08:43,867 | ^ 2021-07-14T22:08:43,868 MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:08:43,868 868 | maxidx = (LASTIDXxfp->buf1size) 2021-07-14T22:08:43,873 | ^ 2021-07-14T22:08:43,877 MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T22:08:43,878 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-14T22:08:43,878 | ^ 2021-07-14T22:08:43,878 MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:08:43,878 1141 | maxidx = (LASTIDXxfp->buf1size) 2021-07-14T22:08:43,885 | ^ 2021-07-14T22:08:43,886 MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:08:43,887 1368 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-14T22:08:43,893 | ^ 2021-07-14T22:08:43,899 MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T22:08:43,899 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-14T22:08:43,899 | ^ 2021-07-14T22:08:43,899 MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T22:08:43,900 1624 | maxidx = (LASTIDX maxsize) 2021-07-14T22:08:45,757 | ^ 2021-07-14T22:08:45,758 MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here 2021-07-14T22:08:45,758 2335 | unsigned int size; 2021-07-14T22:08:45,758 | ^~~~ 2021-07-14T22:08:46,244 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2021-07-14T22:08:46,245 MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-14T22:08:46,245 1157 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2021-07-14T22:08:46,245 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-14T22:08:46,245 MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-14T22:08:46,245 1156 | abs(thiscoord[1] - prevcoord[1]) < larger && 2021-07-14T22:08:46,246 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-14T22:08:46,246 MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-14T22:08:46,246 1155 | abs(thiscoord[0] - prevcoord[0]) < larger && 2021-07-14T22:08:46,246 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-14T22:08:47,093 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2021-07-14T22:08:47,094 MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-14T22:08:47,094 1639 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2021-07-14T22:08:47,095 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-14T22:08:47,095 MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-14T22:08:47,095 1638 | abs(thiscoord[1] - prevcoord[1]) < larger && 2021-07-14T22:08:47,095 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-14T22:08:47,096 MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-14T22:08:47,096 1637 | abs(thiscoord[0] - prevcoord[0]) < larger && 2021-07-14T22:08:47,096 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-14T22:08:48,315 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:08:48,413 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: 2021-07-14T22:08:48,414 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:48,414 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:48,414 | 2021-07-14T22:08:48,422 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2021-07-14T22:08:48,422 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:48,422 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:48,422 | 2021-07-14T22:08:48,422 In file included from MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2021-07-14T22:08:48,423 from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2021-07-14T22:08:48,423 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:48,423 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:48,423 | 2021-07-14T22:08:48,424 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’: 2021-07-14T22:08:48,424 MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T22:08:48,425 78 | if (slen != strlen(version) + 1) 2021-07-14T22:08:48,425 | ^~ 2021-07-14T22:08:48,425 MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T22:08:48,425 86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) 2021-07-14T22:08:48,426 | ^~ 2021-07-14T22:08:48,445 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’: 2021-07-14T22:08:48,445 MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized] 2021-07-14T22:08:48,445 408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); 2021-07-14T22:08:48,446 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:49,636 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:08:49,691 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: 2021-07-14T22:08:49,691 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:49,691 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:49,691 | 2021-07-14T22:08:49,703 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2021-07-14T22:08:49,703 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:49,703 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:49,703 | 2021-07-14T22:08:49,704 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2021-07-14T22:08:49,704 from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2021-07-14T22:08:49,704 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:49,704 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:49,704 | 2021-07-14T22:08:49,859 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 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:08:49,914 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: 2021-07-14T22:08:49,914 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:49,914 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:49,915 | 2021-07-14T22:08:49,926 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2021-07-14T22:08:49,926 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:49,926 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:49,926 | 2021-07-14T22:08:49,927 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2021-07-14T22:08:49,927 from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2021-07-14T22:08:49,927 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-14T22:08:49,927 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-14T22:08:49,927 | 2021-07-14T22:08:50,112 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/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src/xtc_seek.o -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:08:50,365 building 'MDAnalysis.lib.formats.cython_util' extension 2021-07-14T22:08:50,366 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:08:50,773 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:08:50,774 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:08:50,774 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:08:50,774 from MDAnalysis/lib/formats/cython_util.c:623: 2021-07-14T22:08:50,774 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:08:50,775 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:08:50,775 | ^~~~~~~ 2021-07-14T22:08:51,257 MDAnalysis/lib/formats/cython_util.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:08:51,267 MDAnalysis/lib/formats/cython_util.c:20986:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,267 20986 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,268 | ^ 2021-07-14T22:08:51,268 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,268 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,268 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,268 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:51,269 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:51,269 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,280 MDAnalysis/lib/formats/cython_util.c:20986:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,280 20986 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,281 | ^ 2021-07-14T22:08:51,281 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,281 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,281 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,281 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:08:51,281 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:08:51,282 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,293 MDAnalysis/lib/formats/cython_util.c:20986:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,293 20986 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,293 | ^ 2021-07-14T22:08:51,293 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,293 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,294 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,294 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:51,294 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:51,294 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,305 MDAnalysis/lib/formats/cython_util.c:20986:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,305 20986 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,306 | ^ 2021-07-14T22:08:51,306 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,306 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,306 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,306 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:51,306 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:51,306 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,318 MDAnalysis/lib/formats/cython_util.c:20986:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,318 20986 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,318 | ^ 2021-07-14T22:08:51,318 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,318 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,319 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,319 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:08:51,319 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:08:51,319 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,330 MDAnalysis/lib/formats/cython_util.c:20986:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,330 20986 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,330 | ^ 2021-07-14T22:08:51,331 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,331 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,331 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,331 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:51,331 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:51,331 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,345 MDAnalysis/lib/formats/cython_util.c:21002:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,345 21002 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,345 | ^ 2021-07-14T22:08:51,346 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,346 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,346 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,346 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:51,346 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:51,346 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,357 MDAnalysis/lib/formats/cython_util.c:21002:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,358 21002 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,358 | ^ 2021-07-14T22:08:51,358 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,358 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,358 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,358 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:08:51,359 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:08:51,359 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,370 MDAnalysis/lib/formats/cython_util.c:21002:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,370 21002 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,370 | ^ 2021-07-14T22:08:51,370 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,371 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,371 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,371 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:51,371 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:51,371 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,382 MDAnalysis/lib/formats/cython_util.c:21002:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,383 21002 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,383 | ^ 2021-07-14T22:08:51,383 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,383 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,383 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,383 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:51,384 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:51,384 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,395 MDAnalysis/lib/formats/cython_util.c:21002:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,395 21002 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,395 | ^ 2021-07-14T22:08:51,395 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,396 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,396 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,396 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:08:51,396 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:08:51,396 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,407 MDAnalysis/lib/formats/cython_util.c:21002:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,407 21002 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:08:51,408 | ^ 2021-07-14T22:08:51,408 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,408 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,408 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,408 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:08:51,409 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:08:51,409 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:08:51,475 MDAnalysis/lib/formats/cython_util.c: In function ‘__Pyx_decode_c_string’: 2021-07-14T22:08:51,485 MDAnalysis/lib/formats/cython_util.c:21399:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:08:51,485 21399 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-14T22:08:51,485 | ^~~~~~ 2021-07-14T22:08:51,486 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:08:51,486 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:08:51,486 from MDAnalysis/lib/formats/cython_util.c:29: 2021-07-14T22:08:51,486 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-14T22:08:51,486 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-14T22:08:51,486 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,286 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/MDAnalysis/lib/formats/cython_util.o -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:09:11,457 building 'MDAnalysis.analysis.encore.cutils' extension 2021-07-14T22:09:11,458 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-14T22:09:11,458 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-14T22:09:11,459 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:09:11,850 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:09:11,850 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:09:11,850 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:09:11,850 from MDAnalysis/analysis/encore/cutils.c:623: 2021-07-14T22:09:11,850 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:09:11,851 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:09:11,851 | ^~~~~~~ 2021-07-14T22:09:11,961 MDAnalysis/analysis/encore/cutils.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:09:11,963 MDAnalysis/analysis/encore/cutils.c:5113:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,963 5113 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,963 | ^ 2021-07-14T22:09:11,964 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,964 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,964 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,964 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:11,964 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:11,965 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,967 MDAnalysis/analysis/encore/cutils.c:5113:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,967 5113 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,967 | ^ 2021-07-14T22:09:11,967 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,967 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,968 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,968 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:11,968 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:11,968 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,970 MDAnalysis/analysis/encore/cutils.c:5113:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,970 5113 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,970 | ^ 2021-07-14T22:09:11,970 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,971 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,971 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,971 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:11,971 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:11,971 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,973 MDAnalysis/analysis/encore/cutils.c:5113:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,973 5113 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,973 | ^ 2021-07-14T22:09:11,973 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,974 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,974 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,974 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:11,974 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:11,974 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,976 MDAnalysis/analysis/encore/cutils.c:5113:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,976 5113 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,976 | ^ 2021-07-14T22:09:11,976 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,977 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,977 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,977 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:11,977 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:11,977 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,979 MDAnalysis/analysis/encore/cutils.c:5113:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,979 5113 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,979 | ^ 2021-07-14T22:09:11,980 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,980 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,980 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,980 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:11,980 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:11,980 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,983 MDAnalysis/analysis/encore/cutils.c:5129:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,983 5129 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,983 | ^ 2021-07-14T22:09:11,984 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,984 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,984 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,984 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:11,984 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:11,984 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,986 MDAnalysis/analysis/encore/cutils.c:5129:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,986 5129 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,986 | ^ 2021-07-14T22:09:11,987 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,987 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,987 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,987 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:11,987 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:11,987 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,989 MDAnalysis/analysis/encore/cutils.c:5129:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,989 5129 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,990 | ^ 2021-07-14T22:09:11,990 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,990 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,990 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,990 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:11,991 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:11,991 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,993 MDAnalysis/analysis/encore/cutils.c:5129:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,994 5129 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,994 | ^ 2021-07-14T22:09:11,994 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,994 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,994 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,995 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:11,995 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:11,995 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,996 MDAnalysis/analysis/encore/cutils.c:5129:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:11,997 5129 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:11,997 | ^ 2021-07-14T22:09:11,997 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:11,997 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:11,997 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:11,998 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:11,998 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:11,998 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:11,999 MDAnalysis/analysis/encore/cutils.c:5129:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:12,000 5129 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:12,000 | ^ 2021-07-14T22:09:12,000 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:12,000 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:12,001 from MDAnalysis/analysis/encore/cutils.c:29: 2021-07-14T22:09:12,001 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:12,001 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:12,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:14,420 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/MDAnalysis/analysis/encore/cutils.o -o build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:09:14,577 building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension 2021-07-14T22:09:14,578 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-14T22:09:14,579 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/src 2021-07-14T22:09:14,580 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:09:15,051 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:09:15,051 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:09:15,051 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:09:15,051 from MDAnalysis/analysis/encore/clustering/affinityprop.c:629: 2021-07-14T22:09:15,052 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:09:15,052 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:09:15,052 | ^~~~~~~ 2021-07-14T22:09:15,274 MDAnalysis/analysis/encore/clustering/affinityprop.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:09:15,278 MDAnalysis/analysis/encore/clustering/affinityprop.c:6753:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,278 6753 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,279 | ^ 2021-07-14T22:09:15,279 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,279 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,279 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,279 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:15,279 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:15,279 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,283 MDAnalysis/analysis/encore/clustering/affinityprop.c:6753:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,284 6753 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,284 | ^ 2021-07-14T22:09:15,284 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,284 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,284 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,284 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:15,284 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:15,285 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,288 MDAnalysis/analysis/encore/clustering/affinityprop.c:6753:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,288 6753 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,288 | ^ 2021-07-14T22:09:15,289 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,289 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,289 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,289 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:15,289 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:15,289 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,293 MDAnalysis/analysis/encore/clustering/affinityprop.c:6753:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,293 6753 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,293 | ^ 2021-07-14T22:09:15,293 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,293 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,293 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,294 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:15,294 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:15,294 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,297 MDAnalysis/analysis/encore/clustering/affinityprop.c:6753:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,298 6753 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,298 | ^ 2021-07-14T22:09:15,298 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,298 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,298 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,298 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:15,298 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:15,298 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,302 MDAnalysis/analysis/encore/clustering/affinityprop.c:6753:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,302 6753 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,302 | ^ 2021-07-14T22:09:15,302 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,303 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,303 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,303 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:15,303 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:15,303 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,308 MDAnalysis/analysis/encore/clustering/affinityprop.c:6769:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,308 6769 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,308 | ^ 2021-07-14T22:09:15,308 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,309 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,309 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,309 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:15,309 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:15,309 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,312 MDAnalysis/analysis/encore/clustering/affinityprop.c:6769:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,313 6769 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,313 | ^ 2021-07-14T22:09:15,313 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,313 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,313 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,313 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:15,313 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:15,314 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,317 MDAnalysis/analysis/encore/clustering/affinityprop.c:6769:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,317 6769 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,317 | ^ 2021-07-14T22:09:15,318 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,318 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,318 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,318 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:15,318 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:15,318 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,322 MDAnalysis/analysis/encore/clustering/affinityprop.c:6769:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,322 6769 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,322 | ^ 2021-07-14T22:09:15,322 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,322 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,322 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,323 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:15,323 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:15,323 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,326 MDAnalysis/analysis/encore/clustering/affinityprop.c:6769:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,327 6769 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,327 | ^ 2021-07-14T22:09:15,327 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,327 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,327 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,327 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:15,327 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:15,327 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:15,331 MDAnalysis/analysis/encore/clustering/affinityprop.c:6769:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:15,331 6769 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:15,331 | ^ 2021-07-14T22:09:15,331 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:15,332 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:15,332 from MDAnalysis/analysis/encore/clustering/affinityprop.c:35: 2021-07-14T22:09:15,332 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:15,332 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:15,332 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:29,032 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:09:30,203 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/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/src/ap.o -lm -o build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:09:30,362 building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension 2021-07-14T22:09:30,363 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:09:30,364 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/src 2021-07-14T22:09:30,365 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:09:31,152 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -O3 -funroll-loops 2021-07-14T22:09:31,542 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:09:31,543 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:09:31,543 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:09:31,543 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:629: 2021-07-14T22:09:31,543 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:09:31,543 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:09:31,544 | ^~~~~~~ 2021-07-14T22:09:31,666 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-14T22:09:31,668 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5339:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,669 5339 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,669 | ^ 2021-07-14T22:09:31,670 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,670 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,670 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,670 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:31,670 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:31,671 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,674 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5339:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,674 5339 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,674 | ^ 2021-07-14T22:09:31,675 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,675 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,675 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,675 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:31,675 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:31,675 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,678 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5339:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,678 5339 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,678 | ^ 2021-07-14T22:09:31,678 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,679 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,679 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,679 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:31,679 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:31,679 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,681 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5339:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,681 5339 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,681 | ^ 2021-07-14T22:09:31,682 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,682 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,682 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,682 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:31,682 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:31,682 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,684 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5339:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,684 5339 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,685 | ^ 2021-07-14T22:09:31,685 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,685 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,685 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,685 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:31,685 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:31,686 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,687 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5339:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,688 5339 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,688 | ^ 2021-07-14T22:09:31,688 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,688 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,688 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,689 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:31,689 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:31,689 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,692 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5355:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,693 5355 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,693 | ^ 2021-07-14T22:09:31,693 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,693 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,693 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,694 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:31,694 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:31,694 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,696 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5355:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,696 5355 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,696 | ^ 2021-07-14T22:09:31,697 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,697 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,697 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,697 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:31,697 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:31,697 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,699 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5355:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,700 5355 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,700 | ^ 2021-07-14T22:09:31,700 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,700 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,701 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,701 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:31,701 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:31,701 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,703 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5355:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,703 5355 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,704 | ^ 2021-07-14T22:09:31,704 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,704 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,704 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,704 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:31,705 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:31,705 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,707 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5355:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,707 5355 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,707 | ^ 2021-07-14T22:09:31,707 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,707 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,708 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,708 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:31,708 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:31,708 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:31,710 MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:5355:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:31,710 5355 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:31,710 | ^ 2021-07-14T22:09:31,711 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:31,711 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:31,711 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:35: 2021-07-14T22:09:31,711 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:31,711 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:31,711 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:36,124 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/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -lm -o build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:09:36,280 building 'MDAnalysis.lib._cutil' extension 2021-07-14T22:09:36,280 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -std=c++11 2021-07-14T22:09:36,613 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:09:36,613 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:09:36,614 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:09:36,614 from MDAnalysis/lib/_cutil.cpp:643: 2021-07-14T22:09:36,614 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:09:36,614 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:09:36,614 | ^~~~~~~ 2021-07-14T22:09:39,181 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:39,182 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:39,182 from MDAnalysis/lib/_cutil.cpp:35: 2021-07-14T22:09:39,182 MDAnalysis/lib/_cutil.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2021-07-14T22:09:39,182 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,182 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:09:39,182 | ^ 2021-07-14T22:09:39,183 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:09:39,183 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:09:39,183 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,183 MDAnalysis/lib/_cutil.cpp:24123:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,183 24123 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,183 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,183 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:39,184 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:39,184 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,184 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,184 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:09:39,184 | ^ 2021-07-14T22:09:39,184 MDAnalysis/lib/_cutil.cpp:24123:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,185 24123 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,185 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,185 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:39,185 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:39,185 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,185 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,185 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:09:39,185 | ^ 2021-07-14T22:09:39,186 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:09:39,186 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:09:39,186 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,186 MDAnalysis/lib/_cutil.cpp:24123:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,186 24123 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,186 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,186 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:39,186 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:39,187 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,187 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,187 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:09:39,187 | ^ 2021-07-14T22:09:39,187 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:09:39,187 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:09:39,187 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,187 MDAnalysis/lib/_cutil.cpp:24123:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,188 24123 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,188 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,188 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:39,188 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:39,188 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,188 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,188 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:09:39,188 | ^ 2021-07-14T22:09:39,189 MDAnalysis/lib/_cutil.cpp:24123:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,189 24123 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,189 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,189 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:39,189 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:39,189 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,189 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,190 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:09:39,190 | ^ 2021-07-14T22:09:39,190 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:09:39,190 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:09:39,190 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,190 MDAnalysis/lib/_cutil.cpp:24123:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,190 24123 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,190 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,191 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:39,191 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:39,191 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,191 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,191 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:09:39,191 | ^ 2021-07-14T22:09:39,191 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:09:39,192 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:09:39,192 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,192 MDAnalysis/lib/_cutil.cpp:24139:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,192 24139 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,192 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,192 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:39,192 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:39,193 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,193 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,193 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:09:39,193 | ^ 2021-07-14T22:09:39,193 MDAnalysis/lib/_cutil.cpp:24139:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,193 24139 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,193 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,194 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:39,194 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:39,194 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,194 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,194 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:09:39,194 | ^ 2021-07-14T22:09:39,195 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:09:39,196 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:09:39,197 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,198 MDAnalysis/lib/_cutil.cpp:24139:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,199 24139 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,199 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,199 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:39,199 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:39,199 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,199 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,200 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:09:39,200 | ^ 2021-07-14T22:09:39,200 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:09:39,200 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:09:39,200 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,200 MDAnalysis/lib/_cutil.cpp:24139:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,200 24139 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,200 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,200 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:39,201 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:39,201 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,201 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,201 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:09:39,201 | ^ 2021-07-14T22:09:39,201 MDAnalysis/lib/_cutil.cpp:24139:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,201 24139 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,202 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,202 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:09:39,202 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:09:39,202 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,202 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,202 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:09:39,202 | ^ 2021-07-14T22:09:39,203 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:09:39,203 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:09:39,203 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,203 MDAnalysis/lib/_cutil.cpp:24139:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:09:39,203 24139 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:09:39,203 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,203 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:09:39,203 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:09:39,204 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:39,228 MDAnalysis/lib/_cutil.cpp: In function ‘PyObject* __Pyx_decode_c_string(const char*, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))’: 2021-07-14T22:09:39,228 MDAnalysis/lib/_cutil.cpp:25219:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:09:39,228 25219 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-14T22:09:39,228 | ^ 2021-07-14T22:09:39,229 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:09:39,229 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:09:39,229 from MDAnalysis/lib/_cutil.cpp:35: 2021-07-14T22:09:39,229 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-14T22:09:39,229 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-14T22:09:39,229 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,141 In file included from MDAnalysis/lib/_cutil.cpp:654: 2021-07-14T22:09:40,142 MDAnalysis/lib/include/calc_distances.h: At global scope: 2021-07-14T22:09:40,142 MDAnalysis/lib/include/calc_distances.h:833:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,142 833 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,142 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,142 MDAnalysis/lib/include/calc_distances.h:797:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,142 797 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,143 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,143 MDAnalysis/lib/include/calc_distances.h:769:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,143 769 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,143 | ^~~~~~~~~~~~~~ 2021-07-14T22:09:40,143 MDAnalysis/lib/include/calc_distances.h:692:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,144 692 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,144 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,144 MDAnalysis/lib/include/calc_distances.h:649:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,144 649 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,144 | ^~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,144 MDAnalysis/lib/include/calc_distances.h:618:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,145 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,145 | ^~~~~~~~~~~ 2021-07-14T22:09:40,145 MDAnalysis/lib/include/calc_distances.h:593:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,145 593 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,146 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,146 MDAnalysis/lib/include/calc_distances.h:568:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,146 568 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,146 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,147 MDAnalysis/lib/include/calc_distances.h:549:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,147 549 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2021-07-14T22:09:40,147 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,147 MDAnalysis/lib/include/calc_distances.h:494:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,147 494 | static void _calc_self_distance_array_triclinic(coordinate* ref, int numref, 2021-07-14T22:09:40,148 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,148 MDAnalysis/lib/include/calc_distances.h:461:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,148 461 | static void _calc_self_distance_array_ortho(coordinate* ref, int numref, 2021-07-14T22:09:40,148 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,148 MDAnalysis/lib/include/calc_distances.h:434:13: warning: ‘void _calc_self_distance_array(float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,149 434 | static void _calc_self_distance_array(coordinate* ref, int numref, 2021-07-14T22:09:40,149 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,149 MDAnalysis/lib/include/calc_distances.h:407:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,149 407 | static void _calc_distance_array_triclinic(coordinate* ref, int numref, 2021-07-14T22:09:40,149 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,150 MDAnalysis/lib/include/calc_distances.h:380:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,150 380 | static void _calc_distance_array_ortho(coordinate* ref, int numref, coordinate* conf, 2021-07-14T22:09:40,150 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,150 MDAnalysis/lib/include/calc_distances.h:359:13: warning: ‘void _calc_distance_array(float (*)[3], int, float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,150 359 | static void _calc_distance_array(coordinate* ref, int numref, coordinate* conf, 2021-07-14T22:09:40,151 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:09:40,151 MDAnalysis/lib/include/calc_distances.h:90:13: warning: ‘void _ortho_pbc(float (*)[3], int, float*)’ defined but not used [-Wunused-function] 2021-07-14T22:09:40,151 90 | static void _ortho_pbc(coordinate* coords, int numcoords, float* box) 2021-07-14T22:09:40,151 | ^~~~~~~~~~ 2021-07-14T22:10:11,251 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/MDAnalysis/lib/_cutil.o -lm -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:10:11,666 building 'MDAnalysis.lib._augment' extension 2021-07-14T22:10:11,667 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/_augment.o -ffast-math -O3 -funroll-loops -std=c++11 2021-07-14T22:10:11,998 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:10:11,999 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:10:11,999 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:10:11,999 from MDAnalysis/lib/_augment.cpp:638: 2021-07-14T22:10:11,999 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:10:12,000 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:10:12,000 | ^~~~~~~ 2021-07-14T22:10:13,836 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:10:13,836 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:10:13,836 from MDAnalysis/lib/_augment.cpp:30: 2021-07-14T22:10:13,837 MDAnalysis/lib/_augment.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2021-07-14T22:10:13,837 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,837 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:13,838 | ^ 2021-07-14T22:10:13,838 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:13,838 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:10:13,838 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,839 MDAnalysis/lib/_augment.cpp:22962:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,839 22962 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,839 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,839 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:13,840 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:13,840 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,840 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,840 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:10:13,841 | ^ 2021-07-14T22:10:13,841 MDAnalysis/lib/_augment.cpp:22962:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,841 22962 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,841 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,842 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:10:13,842 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:10:13,842 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,842 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,843 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:13,843 | ^ 2021-07-14T22:10:13,843 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:13,843 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:10:13,844 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,844 MDAnalysis/lib/_augment.cpp:22962:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,844 22962 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,845 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,845 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:13,845 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:13,845 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,846 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,846 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:13,846 | ^ 2021-07-14T22:10:13,847 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:13,847 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:10:13,847 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,847 MDAnalysis/lib/_augment.cpp:22962:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,848 22962 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,848 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,848 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:13,848 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:13,849 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,849 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,849 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:10:13,849 | ^ 2021-07-14T22:10:13,850 MDAnalysis/lib/_augment.cpp:22962:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,850 22962 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,850 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,850 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:10:13,851 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:10:13,851 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,851 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,852 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:13,852 | ^ 2021-07-14T22:10:13,852 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:13,852 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:10:13,853 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,853 MDAnalysis/lib/_augment.cpp:22962:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,853 22962 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,853 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,854 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:13,854 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:13,854 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,854 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,855 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:13,855 | ^ 2021-07-14T22:10:13,855 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:13,855 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:10:13,856 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,856 MDAnalysis/lib/_augment.cpp:22978:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,856 22978 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,856 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,857 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:13,857 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:13,857 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,857 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,857 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:10:13,858 | ^ 2021-07-14T22:10:13,858 MDAnalysis/lib/_augment.cpp:22978:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,858 22978 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,859 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,859 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:10:13,859 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:10:13,860 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,860 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,860 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:13,861 | ^ 2021-07-14T22:10:13,861 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:13,861 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:10:13,862 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,862 MDAnalysis/lib/_augment.cpp:22978:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,863 22978 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,863 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,863 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:13,864 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:13,864 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,865 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,865 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:13,865 | ^ 2021-07-14T22:10:13,865 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:13,866 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:10:13,866 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,866 MDAnalysis/lib/_augment.cpp:22978:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,866 22978 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,867 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,867 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:13,867 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:13,868 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,868 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,868 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:10:13,868 | ^ 2021-07-14T22:10:13,869 MDAnalysis/lib/_augment.cpp:22978:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,869 22978 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,869 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,869 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:10:13,870 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:10:13,870 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,870 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,870 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:13,871 | ^ 2021-07-14T22:10:13,871 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:13,871 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:10:13,872 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,872 MDAnalysis/lib/_augment.cpp:22978:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:13,872 22978 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:13,872 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,873 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:13,873 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:13,873 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:13,904 MDAnalysis/lib/_augment.cpp: In function ‘PyObject* __Pyx_decode_c_string(const char*, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))’: 2021-07-14T22:10:13,904 MDAnalysis/lib/_augment.cpp:24185:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:13,904 24185 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-14T22:10:13,905 | ^ 2021-07-14T22:10:13,905 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:10:13,905 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:10:13,906 from MDAnalysis/lib/_augment.cpp:30: 2021-07-14T22:10:13,906 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-14T22:10:13,906 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-14T22:10:13,906 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:42,718 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/MDAnalysis/lib/_augment.o -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:10:43,115 building 'MDAnalysis.lib.nsgrid' extension 2021-07-14T22:10:43,115 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 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/nsgrid.o -ffast-math -O3 -funroll-loops -std=c++11 2021-07-14T22:10:43,512 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T22:10:43,512 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T22:10:43,513 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T22:10:43,513 from MDAnalysis/lib/nsgrid.cpp:644: 2021-07-14T22:10:43,513 /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-14T22:10:43,514 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T22:10:43,514 | ^~~~~~~ 2021-07-14T22:10:45,558 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:10:45,558 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:10:45,558 from MDAnalysis/lib/nsgrid.cpp:30: 2021-07-14T22:10:45,559 MDAnalysis/lib/nsgrid.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2021-07-14T22:10:45,559 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,559 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:45,559 | ^ 2021-07-14T22:10:45,560 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:45,560 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:10:45,560 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,560 MDAnalysis/lib/nsgrid.cpp:29022:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,561 29022 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,561 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,561 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:45,562 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:45,562 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,562 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,562 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:10:45,563 | ^ 2021-07-14T22:10:45,563 MDAnalysis/lib/nsgrid.cpp:29022:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,563 29022 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,563 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,564 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:10:45,564 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:10:45,564 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,565 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,565 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:45,565 | ^ 2021-07-14T22:10:45,566 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:45,566 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:10:45,566 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,566 MDAnalysis/lib/nsgrid.cpp:29022:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,567 29022 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,567 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,567 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:45,568 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:45,568 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,568 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,569 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:45,569 | ^ 2021-07-14T22:10:45,569 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:45,569 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:10:45,570 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,570 MDAnalysis/lib/nsgrid.cpp:29022:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,570 29022 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,571 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,571 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:45,571 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:45,571 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,572 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,572 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:10:45,572 | ^ 2021-07-14T22:10:45,573 MDAnalysis/lib/nsgrid.cpp:29022:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,573 29022 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,573 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,574 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:10:45,574 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:10:45,574 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,574 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,575 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:45,575 | ^ 2021-07-14T22:10:45,575 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:45,576 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:10:45,576 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,576 MDAnalysis/lib/nsgrid.cpp:29022:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,576 29022 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,577 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,577 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:45,577 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:45,578 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,578 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,578 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:45,579 | ^ 2021-07-14T22:10:45,579 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:45,579 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:10:45,579 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,580 MDAnalysis/lib/nsgrid.cpp:29038:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,580 29038 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,580 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,581 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:45,581 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:45,581 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,582 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,582 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:10:45,582 | ^ 2021-07-14T22:10:45,582 MDAnalysis/lib/nsgrid.cpp:29038:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,583 29038 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,583 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,583 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:10:45,584 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:10:45,584 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,584 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,585 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:45,585 | ^ 2021-07-14T22:10:45,585 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:45,585 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:10:45,586 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,586 MDAnalysis/lib/nsgrid.cpp:29038:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,586 29038 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,587 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,587 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:45,587 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:45,588 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,588 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,588 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:45,588 | ^ 2021-07-14T22:10:45,589 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:45,589 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T22:10:45,589 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,590 MDAnalysis/lib/nsgrid.cpp:29038:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,590 29038 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,590 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,590 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:45,591 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:45,591 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,591 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,591 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T22:10:45,592 | ^ 2021-07-14T22:10:45,592 MDAnalysis/lib/nsgrid.cpp:29038:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,592 29038 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,593 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,593 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T22:10:45,593 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T22:10:45,594 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,594 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,594 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T22:10:45,594 | ^ 2021-07-14T22:10:45,595 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T22:10:45,595 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T22:10:45,595 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,595 MDAnalysis/lib/nsgrid.cpp:29038:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T22:10:45,596 29038 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T22:10:45,596 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,596 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T22:10:45,597 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T22:10:45,597 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:10:45,629 MDAnalysis/lib/nsgrid.cpp: In function ‘PyObject* __Pyx_decode_c_string(const char*, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))’: 2021-07-14T22:10:45,629 MDAnalysis/lib/nsgrid.cpp:30555:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T22:10:45,629 30555 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-14T22:10:45,630 | ^ 2021-07-14T22:10:45,630 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T22:10:45,630 from /usr/include/python3.9/Python.h:97, 2021-07-14T22:10:45,631 from MDAnalysis/lib/nsgrid.cpp:30: 2021-07-14T22:10:45,631 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-14T22:10:45,631 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-14T22:10:45,631 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T22:11:15,285 In file included from /usr/include/c++/10/vector:72, 2021-07-14T22:11:15,285 from MDAnalysis/lib/nsgrid.cpp:641: 2021-07-14T22:11:15,286 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2021-07-14T22:11:15,286 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-14T22:11:15,286 426 | vector<_Tp, _Alloc>:: 2021-07-14T22:11:15,287 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T22:11:15,327 In file included from /usr/include/c++/10/vector:67, 2021-07-14T22:11:15,327 from MDAnalysis/lib/nsgrid.cpp:641: 2021-07-14T22:11:15,328 /usr/include/c++/10/bits/stl_vector.h: In function ‘void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_add_neighbors(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int, __pyx_t_10MDAnalysis_3lib_6nsgrid_ns_int, __pyx_t_10MDAnalysis_3lib_6nsgrid_dreal)’: 2021-07-14T22:11:15,328 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-14T22:11:15,328 1198 | _M_realloc_insert(end(), __x); 2021-07-14T22:11:15,328 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-14T22:11:16,515 /usr/include/c++/10/bits/stl_vector.h: In function ‘void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_create_buffers(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*)’: 2021-07-14T22:11:16,515 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-14T22:11:16,516 1198 | _M_realloc_insert(end(), __x); 2021-07-14T22:11:16,516 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-14T22:11:23,158 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/MDAnalysis/lib/nsgrid.o -o build/lib.linux-armv7l-3.9/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so 2021-07-14T22:11:23,592 installing to build/bdist.linux-armv7l/wheel 2021-07-14T22:11:23,592 running install 2021-07-14T22:11:23,593 running install_lib 2021-07-14T22:11:23,598 creating build/bdist.linux-armv7l 2021-07-14T22:11:23,599 creating build/bdist.linux-armv7l/wheel 2021-07-14T22:11:23,600 creating build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-14T22:11:23,602 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,603 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,606 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,608 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,611 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,613 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,616 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,619 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/_elements.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,621 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,624 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,627 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,629 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,633 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,636 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,638 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,641 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,643 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,646 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,649 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,652 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,654 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,657 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-14T22:11:23,658 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-14T22:11:23,661 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-14T22:11:23,663 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-14T22:11:23,667 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-14T22:11:23,669 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,672 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,674 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,677 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,679 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,682 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-14T22:11:23,684 copying build/lib.linux-armv7l-3.9/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-14T22:11:23,687 creating build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,688 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,692 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/AtomGroup.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,695 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,697 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,701 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,705 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,707 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,709 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,716 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,719 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/qcprot.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,721 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,724 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,726 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,728 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,730 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/parallel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,732 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-14T22:11:23,737 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,738 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,776 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,780 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,789 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,792 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,845 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,848 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,851 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,855 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2021-07-14T22:11:23,856 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2021-07-14T22:11:23,884 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2021-07-14T22:11:23,933 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2021-07-14T22:11:23,982 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2021-07-14T22:11:23,984 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:23,992 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:24,035 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:24,039 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:24,042 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:24,050 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:24,088 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-14T22:11:24,101 copying build/lib.linux-armv7l-3.9/MDAnalysis/KDTree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-14T22:11:24,103 creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-14T22:11:24,104 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-14T22:11:24,107 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-14T22:11:24,110 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-14T22:11:24,113 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,114 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,117 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,120 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,123 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,125 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,128 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,130 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,134 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,139 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,145 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,147 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,150 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,152 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,155 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,159 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,161 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,163 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,167 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,170 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,173 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,175 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,181 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,184 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,187 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,189 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,192 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,195 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-14T22:11:24,198 copying build/lib.linux-armv7l-3.9/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-14T22:11:24,200 copying build/lib.linux-armv7l-3.9/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-14T22:11:24,203 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,204 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,207 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,211 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2021-07-14T22:11:24,211 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2021-07-14T22:11:24,214 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2021-07-14T22:11:24,217 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,220 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,223 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,226 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-14T22:11:24,227 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-14T22:11:24,232 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-14T22:11:24,239 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-14T22:11:24,244 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-14T22:11:24,246 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,250 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,252 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,256 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/helanal.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,261 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-14T22:11:24,262 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-14T22:11:24,266 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-14T22:11:24,268 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-14T22:11:24,271 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-14T22:11:24,273 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-14T22:11:24,274 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-14T22:11:24,280 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-14T22:11:24,283 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-14T22:11:24,286 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-14T22:11:24,287 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-14T22:11:24,290 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-14T22:11:24,292 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-14T22:11:24,295 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-14T22:11:24,308 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-14T22:11:24,311 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-14T22:11:24,317 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:11:24,318 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:11:24,327 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:11:24,330 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:11:24,333 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-14T22:11:24,335 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-14T22:11:24,338 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-14T22:11:24,341 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-14T22:11:24,344 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,346 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,349 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,353 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,358 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,362 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,364 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,367 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,370 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,372 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,376 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,380 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-14T22:11:24,383 copying build/lib.linux-armv7l-3.9/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-14T22:11:24,385 copying build/lib.linux-armv7l-3.9/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-14T22:11:24,388 creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-14T22:11:24,389 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-14T22:11:24,393 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-14T22:11:24,395 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-14T22:11:24,399 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-14T22:11:24,401 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-14T22:11:24,405 creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-14T22:11:24,406 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-14T22:11:24,408 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-14T22:11:24,410 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-14T22:11:24,413 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-14T22:11:24,415 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-14T22:11:24,417 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-14T22:11:24,420 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-14T22:11:24,422 creating build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-14T22:11:24,423 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/ten2eleven.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-14T22:11:24,426 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/test_dummy_torsion.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-14T22:11:24,429 creating build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,429 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,432 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_agmethods.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,434 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_torsions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,436 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_numframes.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,438 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_calctorsions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,440 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_writer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,442 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_camelcase.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,444 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,446 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_agmethods2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,449 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,450 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,453 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,455 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_mdaimports.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,457 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_selectatoms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,459 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-14T22:11:24,461 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-14T22:11:24,463 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-14T22:11:24,466 copying build/lib.linux-armv7l-3.9/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-14T22:11:24,470 creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-14T22:11:24,471 copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-14T22:11:24,477 copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-14T22:11:24,481 copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-14T22:11:24,484 copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-14T22:11:24,487 creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-14T22:11:24,488 copying build/lib.linux-armv7l-3.9/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-14T22:11:24,491 copying build/lib.linux-armv7l-3.9/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-14T22:11:24,493 running install_egg_info 2021-07-14T22:11:24,519 running egg_info 2021-07-14T22:11:24,520 writing MDAnalysis.egg-info/PKG-INFO 2021-07-14T22:11:24,523 writing dependency_links to MDAnalysis.egg-info/dependency_links.txt 2021-07-14T22:11:24,525 writing requirements to MDAnalysis.egg-info/requires.txt 2021-07-14T22:11:24,526 writing top-level names to MDAnalysis.egg-info/top_level.txt 2021-07-14T22:11:24,629 reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2021-07-14T22:11:24,691 reading manifest template 'MANIFEST.in' 2021-07-14T22:11:24,834 warning: no files found matching 'MDAnalysis/coordinates/xdrfile/src/*' 2021-07-14T22:11:24,834 warning: no files found matching 'MDAnalysis/lib/src/pyqcprot/*' 2021-07-14T22:11:24,918 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-14T22:11:24,920 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2021-07-14T22:11:24,922 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2021-07-14T22:11:24,925 warning: no previously-included files matching '*~' found anywhere in distribution 2021-07-14T22:11:24,925 adding license file 'LICENSE' 2021-07-14T22:11:24,925 adding license file 'AUTHORS' 2021-07-14T22:11:24,947 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2021-07-14T22:11:24,949 Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-0.20.1-py3.9.egg-info 2021-07-14T22:11:24,963 running install_scripts 2021-07-14T22:11:25,075 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-14T22:11:25,076 adding license file "AUTHORS" (matched pattern "AUTHORS*") 2021-07-14T22:11:25,083 creating build/bdist.linux-armv7l/wheel/MDAnalysis-0.20.1.dist-info/WHEEL 2021-07-14T22:11:25,086 creating '/tmp/pip-wheel-0pbp0cpp/MDAnalysis-0.20.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-14T22:11:25,089 adding 'MDAnalysis/KDTree.py' 2021-07-14T22:11:25,091 adding 'MDAnalysis/__init__.py' 2021-07-14T22:11:25,092 adding 'MDAnalysis/authors.py' 2021-07-14T22:11:25,094 adding 'MDAnalysis/due.py' 2021-07-14T22:11:25,095 adding 'MDAnalysis/exceptions.py' 2021-07-14T22:11:25,098 adding 'MDAnalysis/units.py' 2021-07-14T22:11:25,099 adding 'MDAnalysis/version.py' 2021-07-14T22:11:25,101 adding 'MDAnalysis/analysis/__init__.py' 2021-07-14T22:11:25,109 adding 'MDAnalysis/analysis/align.py' 2021-07-14T22:11:25,112 adding 'MDAnalysis/analysis/base.py' 2021-07-14T22:11:25,115 adding 'MDAnalysis/analysis/contacts.py' 2021-07-14T22:11:25,122 adding 'MDAnalysis/analysis/density.py' 2021-07-14T22:11:25,125 adding 'MDAnalysis/analysis/diffusionmap.py' 2021-07-14T22:11:25,128 adding 'MDAnalysis/analysis/dihedrals.py' 2021-07-14T22:11:25,130 adding 'MDAnalysis/analysis/distances.py' 2021-07-14T22:11:25,132 adding 'MDAnalysis/analysis/gnm.py' 2021-07-14T22:11:25,137 adding 'MDAnalysis/analysis/helanal.py' 2021-07-14T22:11:25,146 adding 'MDAnalysis/analysis/hole.py' 2021-07-14T22:11:25,148 adding 'MDAnalysis/analysis/leaflet.py' 2021-07-14T22:11:25,151 adding 'MDAnalysis/analysis/lineardensity.py' 2021-07-14T22:11:25,153 adding 'MDAnalysis/analysis/nuclinfo.py' 2021-07-14T22:11:25,156 adding 'MDAnalysis/analysis/pca.py' 2021-07-14T22:11:25,158 adding 'MDAnalysis/analysis/polymer.py' 2021-07-14T22:11:25,169 adding 'MDAnalysis/analysis/psa.py' 2021-07-14T22:11:25,172 adding 'MDAnalysis/analysis/rdf.py' 2021-07-14T22:11:25,177 adding 'MDAnalysis/analysis/rms.py' 2021-07-14T22:11:25,183 adding 'MDAnalysis/analysis/waterdynamics.py' 2021-07-14T22:11:25,185 adding 'MDAnalysis/analysis/x3dna.py' 2021-07-14T22:11:25,186 adding 'MDAnalysis/analysis/data/__init__.py' 2021-07-14T22:11:25,188 adding 'MDAnalysis/analysis/data/filenames.py' 2021-07-14T22:11:25,191 adding 'MDAnalysis/analysis/data/janin_ref_data.npy' 2021-07-14T22:11:25,197 adding 'MDAnalysis/analysis/data/rama_ref_data.npy' 2021-07-14T22:11:25,199 adding 'MDAnalysis/analysis/encore/__init__.py' 2021-07-14T22:11:25,201 adding 'MDAnalysis/analysis/encore/bootstrap.py' 2021-07-14T22:11:25,203 adding 'MDAnalysis/analysis/encore/confdistmatrix.py' 2021-07-14T22:11:25,205 adding 'MDAnalysis/analysis/encore/covariance.py' 2021-07-14T22:11:25,237 adding 'MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:25,245 adding 'MDAnalysis/analysis/encore/similarity.py' 2021-07-14T22:11:25,247 adding 'MDAnalysis/analysis/encore/utils.py' 2021-07-14T22:11:25,250 adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' 2021-07-14T22:11:25,252 adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' 2021-07-14T22:11:25,253 adding 'MDAnalysis/analysis/encore/clustering/__init__.py' 2021-07-14T22:11:25,358 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:25,364 adding 'MDAnalysis/analysis/encore/clustering/cluster.py' 2021-07-14T22:11:25,366 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' 2021-07-14T22:11:25,367 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' 2021-07-14T22:11:25,369 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' 2021-07-14T22:11:25,431 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:25,434 adding 'MDAnalysis/analysis/hbonds/__init__.py' 2021-07-14T22:11:25,442 adding 'MDAnalysis/analysis/hbonds/hbond_analysis.py' 2021-07-14T22:11:25,446 adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' 2021-07-14T22:11:25,455 adding 'MDAnalysis/analysis/hbonds/wbridge_analysis.py' 2021-07-14T22:11:25,457 adding 'MDAnalysis/analysis/legacy/__init__.py' 2021-07-14T22:11:25,461 adding 'MDAnalysis/analysis/legacy/x3dna.py' 2021-07-14T22:11:25,464 adding 'MDAnalysis/auxiliary/XVG.py' 2021-07-14T22:11:25,467 adding 'MDAnalysis/auxiliary/__init__.py' 2021-07-14T22:11:25,471 adding 'MDAnalysis/auxiliary/base.py' 2021-07-14T22:11:25,473 adding 'MDAnalysis/auxiliary/core.py' 2021-07-14T22:11:25,475 adding 'MDAnalysis/coordinates/CRD.py' 2021-07-14T22:11:25,478 adding 'MDAnalysis/coordinates/DCD.py' 2021-07-14T22:11:25,480 adding 'MDAnalysis/coordinates/DLPoly.py' 2021-07-14T22:11:25,482 adding 'MDAnalysis/coordinates/DMS.py' 2021-07-14T22:11:25,483 adding 'MDAnalysis/coordinates/GMS.py' 2021-07-14T22:11:25,486 adding 'MDAnalysis/coordinates/GRO.py' 2021-07-14T22:11:25,488 adding 'MDAnalysis/coordinates/GSD.py' 2021-07-14T22:11:25,489 adding 'MDAnalysis/coordinates/INPCRD.py' 2021-07-14T22:11:25,492 adding 'MDAnalysis/coordinates/LAMMPS.py' 2021-07-14T22:11:25,494 adding 'MDAnalysis/coordinates/MMTF.py' 2021-07-14T22:11:25,496 adding 'MDAnalysis/coordinates/MOL2.py' 2021-07-14T22:11:25,502 adding 'MDAnalysis/coordinates/PDB.py' 2021-07-14T22:11:25,505 adding 'MDAnalysis/coordinates/PDBQT.py' 2021-07-14T22:11:25,507 adding 'MDAnalysis/coordinates/PQR.py' 2021-07-14T22:11:25,513 adding 'MDAnalysis/coordinates/TRJ.py' 2021-07-14T22:11:25,515 adding 'MDAnalysis/coordinates/TRR.py' 2021-07-14T22:11:25,518 adding 'MDAnalysis/coordinates/TRZ.py' 2021-07-14T22:11:25,520 adding 'MDAnalysis/coordinates/TXYZ.py' 2021-07-14T22:11:25,522 adding 'MDAnalysis/coordinates/XDR.py' 2021-07-14T22:11:25,523 adding 'MDAnalysis/coordinates/XTC.py' 2021-07-14T22:11:25,526 adding 'MDAnalysis/coordinates/XYZ.py' 2021-07-14T22:11:25,531 adding 'MDAnalysis/coordinates/__init__.py' 2021-07-14T22:11:25,541 adding 'MDAnalysis/coordinates/base.py' 2021-07-14T22:11:25,545 adding 'MDAnalysis/coordinates/chain.py' 2021-07-14T22:11:25,547 adding 'MDAnalysis/coordinates/core.py' 2021-07-14T22:11:25,550 adding 'MDAnalysis/coordinates/memory.py' 2021-07-14T22:11:25,552 adding 'MDAnalysis/coordinates/null.py' 2021-07-14T22:11:25,554 adding 'MDAnalysis/core/AtomGroup.py' 2021-07-14T22:11:25,556 adding 'MDAnalysis/core/__init__.py' 2021-07-14T22:11:25,558 adding 'MDAnalysis/core/_get_readers.py' 2021-07-14T22:11:25,559 adding 'MDAnalysis/core/distances.py' 2021-07-14T22:11:25,580 adding 'MDAnalysis/core/groups.py' 2021-07-14T22:11:25,582 adding 'MDAnalysis/core/log.py' 2021-07-14T22:11:25,584 adding 'MDAnalysis/core/parallel.py' 2021-07-14T22:11:25,585 adding 'MDAnalysis/core/qcprot.py' 2021-07-14T22:11:25,589 adding 'MDAnalysis/core/selection.py' 2021-07-14T22:11:25,592 adding 'MDAnalysis/core/topology.py' 2021-07-14T22:11:25,599 adding 'MDAnalysis/core/topologyattrs.py' 2021-07-14T22:11:25,604 adding 'MDAnalysis/core/topologyobjects.py' 2021-07-14T22:11:25,605 adding 'MDAnalysis/core/transformations.py' 2021-07-14T22:11:25,607 adding 'MDAnalysis/core/units.py' 2021-07-14T22:11:25,613 adding 'MDAnalysis/core/universe.py' 2021-07-14T22:11:25,615 adding 'MDAnalysis/core/util.py' 2021-07-14T22:11:25,617 adding 'MDAnalysis/lib/NeighborSearch.py' 2021-07-14T22:11:25,618 adding 'MDAnalysis/lib/__init__.py' 2021-07-14T22:11:25,903 adding 'MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:26,264 adding 'MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:26,334 adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:26,598 adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:26,666 adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:26,674 adding 'MDAnalysis/lib/distances.py' 2021-07-14T22:11:26,677 adding 'MDAnalysis/lib/log.py' 2021-07-14T22:11:26,679 adding 'MDAnalysis/lib/mdamath.py' 2021-07-14T22:11:27,097 adding 'MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:27,117 adding 'MDAnalysis/lib/pkdtree.py' 2021-07-14T22:11:27,184 adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:27,194 adding 'MDAnalysis/lib/transformations.py' 2021-07-14T22:11:27,206 adding 'MDAnalysis/lib/util.py' 2021-07-14T22:11:27,208 adding 'MDAnalysis/lib/formats/__init__.py' 2021-07-14T22:11:27,426 adding 'MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:27,866 adding 'MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:28,315 adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T22:11:28,333 adding 'MDAnalysis/migration/__init__.py' 2021-07-14T22:11:28,334 adding 'MDAnalysis/migration/ten2eleven.py' 2021-07-14T22:11:28,336 adding 'MDAnalysis/migration/test_dummy_old_MDA_code.py' 2021-07-14T22:11:28,337 adding 'MDAnalysis/migration/test_dummy_torsion.py' 2021-07-14T22:11:28,339 adding 'MDAnalysis/migration/fixes/__init__.py' 2021-07-14T22:11:28,340 adding 'MDAnalysis/migration/fixes/fix_agcountmethods.py' 2021-07-14T22:11:28,341 adding 'MDAnalysis/migration/fixes/fix_agmethods.py' 2021-07-14T22:11:28,343 adding 'MDAnalysis/migration/fixes/fix_agmethods2.py' 2021-07-14T22:11:28,344 adding 'MDAnalysis/migration/fixes/fix_agsetterpluralization.py' 2021-07-14T22:11:28,346 adding 'MDAnalysis/migration/fixes/fix_calctorsions.py' 2021-07-14T22:11:28,347 adding 'MDAnalysis/migration/fixes/fix_camelcase.py' 2021-07-14T22:11:28,349 adding 'MDAnalysis/migration/fixes/fix_framenumberingzerobased.py' 2021-07-14T22:11:28,350 adding 'MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py' 2021-07-14T22:11:28,351 adding 'MDAnalysis/migration/fixes/fix_mdaimports.py' 2021-07-14T22:11:28,353 adding 'MDAnalysis/migration/fixes/fix_numframes.py' 2021-07-14T22:11:28,354 adding 'MDAnalysis/migration/fixes/fix_selectatoms.py' 2021-07-14T22:11:28,356 adding 'MDAnalysis/migration/fixes/fix_torsionclasses.py' 2021-07-14T22:11:28,357 adding 'MDAnalysis/migration/fixes/fix_torsions.py' 2021-07-14T22:11:28,359 adding 'MDAnalysis/migration/fixes/fix_writer.py' 2021-07-14T22:11:28,361 adding 'MDAnalysis/selections/__init__.py' 2021-07-14T22:11:28,363 adding 'MDAnalysis/selections/base.py' 2021-07-14T22:11:28,364 adding 'MDAnalysis/selections/charmm.py' 2021-07-14T22:11:28,366 adding 'MDAnalysis/selections/gromacs.py' 2021-07-14T22:11:28,368 adding 'MDAnalysis/selections/jmol.py' 2021-07-14T22:11:28,369 adding 'MDAnalysis/selections/pymol.py' 2021-07-14T22:11:28,371 adding 'MDAnalysis/selections/vmd.py' 2021-07-14T22:11:28,373 adding 'MDAnalysis/tests/__init__.py' 2021-07-14T22:11:28,374 adding 'MDAnalysis/tests/datafiles.py' 2021-07-14T22:11:28,377 adding 'MDAnalysis/topology/CRDParser.py' 2021-07-14T22:11:28,378 adding 'MDAnalysis/topology/DLPolyParser.py' 2021-07-14T22:11:28,380 adding 'MDAnalysis/topology/DMSParser.py' 2021-07-14T22:11:28,382 adding 'MDAnalysis/topology/ExtendedPDBParser.py' 2021-07-14T22:11:28,384 adding 'MDAnalysis/topology/GMSParser.py' 2021-07-14T22:11:28,385 adding 'MDAnalysis/topology/GROParser.py' 2021-07-14T22:11:28,387 adding 'MDAnalysis/topology/GSDParser.py' 2021-07-14T22:11:28,389 adding 'MDAnalysis/topology/HoomdXMLParser.py' 2021-07-14T22:11:28,393 adding 'MDAnalysis/topology/LAMMPSParser.py' 2021-07-14T22:11:28,395 adding 'MDAnalysis/topology/MMTFParser.py' 2021-07-14T22:11:28,397 adding 'MDAnalysis/topology/MOL2Parser.py' 2021-07-14T22:11:28,399 adding 'MDAnalysis/topology/MinimalParser.py' 2021-07-14T22:11:28,401 adding 'MDAnalysis/topology/PDBParser.py' 2021-07-14T22:11:28,403 adding 'MDAnalysis/topology/PDBQTParser.py' 2021-07-14T22:11:28,405 adding 'MDAnalysis/topology/PQRParser.py' 2021-07-14T22:11:28,408 adding 'MDAnalysis/topology/PSFParser.py' 2021-07-14T22:11:28,411 adding 'MDAnalysis/topology/TOPParser.py' 2021-07-14T22:11:28,413 adding 'MDAnalysis/topology/TPRParser.py' 2021-07-14T22:11:28,415 adding 'MDAnalysis/topology/TXYZParser.py' 2021-07-14T22:11:28,417 adding 'MDAnalysis/topology/XYZParser.py' 2021-07-14T22:11:28,419 adding 'MDAnalysis/topology/__init__.py' 2021-07-14T22:11:28,421 adding 'MDAnalysis/topology/_elements.py' 2021-07-14T22:11:28,423 adding 'MDAnalysis/topology/base.py' 2021-07-14T22:11:28,425 adding 'MDAnalysis/topology/core.py' 2021-07-14T22:11:28,427 adding 'MDAnalysis/topology/guessers.py' 2021-07-14T22:11:28,430 adding 'MDAnalysis/topology/tables.py' 2021-07-14T22:11:28,431 adding 'MDAnalysis/topology/tpr/__init__.py' 2021-07-14T22:11:28,433 adding 'MDAnalysis/topology/tpr/obj.py' 2021-07-14T22:11:28,435 adding 'MDAnalysis/topology/tpr/setting.py' 2021-07-14T22:11:28,440 adding 'MDAnalysis/topology/tpr/utils.py' 2021-07-14T22:11:28,442 adding 'MDAnalysis/transformations/__init__.py' 2021-07-14T22:11:28,444 adding 'MDAnalysis/transformations/fit.py' 2021-07-14T22:11:28,446 adding 'MDAnalysis/transformations/positionaveraging.py' 2021-07-14T22:11:28,448 adding 'MDAnalysis/transformations/rotate.py' 2021-07-14T22:11:28,450 adding 'MDAnalysis/transformations/translate.py' 2021-07-14T22:11:28,452 adding 'MDAnalysis/visualization/__init__.py' 2021-07-14T22:11:28,454 adding 'MDAnalysis/visualization/streamlines.py' 2021-07-14T22:11:28,458 adding 'MDAnalysis/visualization/streamlines_3D.py' 2021-07-14T22:11:28,461 adding 'MDAnalysis-0.20.1.dist-info/AUTHORS' 2021-07-14T22:11:28,465 adding 'MDAnalysis-0.20.1.dist-info/LICENSE' 2021-07-14T22:11:28,467 adding 'MDAnalysis-0.20.1.dist-info/METADATA' 2021-07-14T22:11:28,468 adding 'MDAnalysis-0.20.1.dist-info/WHEEL' 2021-07-14T22:11:28,469 adding 'MDAnalysis-0.20.1.dist-info/top_level.txt' 2021-07-14T22:11:28,472 adding 'MDAnalysis-0.20.1.dist-info/RECORD' 2021-07-14T22:11:28,552 removing build/bdist.linux-armv7l/wheel 2021-07-14T22:11:28,765 Building wheel for mdanalysis (setup.py): finished with status 'done' 2021-07-14T22:11:28,854 Created wheel for mdanalysis: filename=MDAnalysis-0.20.1-cp39-cp39-linux_armv7l.whl size=5826356 sha256=89f6feff5fc44ebffd65aa746c268db44a975620306dfebc09a8e7b8e9d5e4da 2021-07-14T22:11:28,855 Stored in directory: /tmp/pip-ephem-wheel-cache-mvtcbn_o/wheels/f7/c7/fc/de691647fcb56dd73b8aad6212f40c1d5f980c1dd08de73d75 2021-07-14T22:11:28,878 Successfully built mdanalysis 2021-07-14T22:11:29,066 Removed build tracker: '/tmp/pip-req-tracker-6k4v2ikl'