2021-07-16T08:03:24,874 Created temporary directory: /tmp/pip-ephem-wheel-cache-4x8_fxvz
2021-07-16T08:03:24,877 Created temporary directory: /tmp/pip-req-tracker-mbws08l1
2021-07-16T08:03:24,877 Initialized build tracking at /tmp/pip-req-tracker-mbws08l1
2021-07-16T08:03:24,878 Created build tracker: /tmp/pip-req-tracker-mbws08l1
2021-07-16T08:03:24,878 Entered build tracker: /tmp/pip-req-tracker-mbws08l1
2021-07-16T08:03:24,878 Created temporary directory: /tmp/pip-wheel-g1n8ix0t
2021-07-16T08:03:24,908 1 location(s) to search for versions of mdanalysis:
2021-07-16T08:03:24,908 * https://pypi.org/simple/mdanalysis/
2021-07-16T08:03:24,908 Fetching project page and analyzing links: https://pypi.org/simple/mdanalysis/
2021-07-16T08:03:24,909 Getting page https://pypi.org/simple/mdanalysis/
2021-07-16T08:03:24,910 Found index url https://pypi.org/simple
2021-07-16T08:03:25,107   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
2021-07-16T08:03:25,107   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
2021-07-16T08:03:25,107   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
2021-07-16T08:03:25,108   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
2021-07-16T08:03:25,108   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
2021-07-16T08:03:25,108   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
2021-07-16T08:03:25,109   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
2021-07-16T08:03:25,109   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
2021-07-16T08:03:25,109   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
2021-07-16T08:03:25,109   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
2021-07-16T08:03:25,110   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
2021-07-16T08:03:25,110   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
2021-07-16T08:03:25,110   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
2021-07-16T08:03:25,111   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
2021-07-16T08:03:25,111   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
2021-07-16T08:03:25,111   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
2021-07-16T08:03:25,111   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
2021-07-16T08:03:25,112   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
2021-07-16T08:03:25,112   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
2021-07-16T08:03:25,112   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
2021-07-16T08:03:25,112   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
2021-07-16T08:03:25,113   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
2021-07-16T08:03:25,113   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
2021-07-16T08:03:25,113   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
2021-07-16T08:03:25,114   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
2021-07-16T08:03:25,114   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
2021-07-16T08:03:25,114   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
2021-07-16T08:03:25,116   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)
2021-07-16T08:03:25,117   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)
2021-07-16T08:03:25,118   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)
2021-07-16T08:03:25,119   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
2021-07-16T08:03:25,119 Skipping link: not a file: https://pypi.org/simple/mdanalysis/
2021-07-16T08:03:25,140 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates
2021-07-16T08:03:25,160 Collecting mdanalysis==1.0.0
2021-07-16T08:03:25,161   Created temporary directory: /tmp/pip-unpack-ylp8_hy9
2021-07-16T08:03:25,200   Downloading MDAnalysis-1.0.0.tar.gz (19.6 MB)
2021-07-16T08:03:32,988   Added mdanalysis==1.0.0 from https://files.pythonhosted.org/packages/c9/ae/11905971cc6cdb436bff040270f58fb3fc54ef77aea2ce2dfc269129f74e/MDAnalysis-1.0.0.tar.gz#sha256=f45a024aca45e390ff1c45ca90beb2180b78881be377e2a1aa9cd6c109bcfa81 to build tracker '/tmp/pip-req-tracker-mbws08l1'
2021-07-16T08:03:32,990     Running setup.py (path:/tmp/pip-wheel-g1n8ix0t/mdanalysis_50498136201448a3b5abe4aafa6868ec/setup.py) egg_info for package mdanalysis
2021-07-16T08:03:32,991     Created temporary directory: /tmp/pip-pip-egg-info-86e5dtew
2021-07-16T08:03:32,991     Running command python setup.py egg_info
2021-07-16T08:03:34,231     /tmp/pip-wheel-g1n8ix0t/mdanalysis_50498136201448a3b5abe4aafa6868ec/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.
2021-07-16T08:03:34,232       self.config = configparser.SafeConfigParser()
2021-07-16T08:03:34,809     Attempting to autodetect OpenMP support... Compiler supports OpenMP
2021-07-16T08:03:34,809     Will not attempt to use Cython.
2021-07-16T08:03:34,810     running egg_info
2021-07-16T08:03:34,811     creating /tmp/pip-pip-egg-info-86e5dtew/MDAnalysis.egg-info
2021-07-16T08:03:34,813     writing /tmp/pip-pip-egg-info-86e5dtew/MDAnalysis.egg-info/PKG-INFO
2021-07-16T08:03:34,816     writing dependency_links to /tmp/pip-pip-egg-info-86e5dtew/MDAnalysis.egg-info/dependency_links.txt
2021-07-16T08:03:34,818     writing requirements to /tmp/pip-pip-egg-info-86e5dtew/MDAnalysis.egg-info/requires.txt
2021-07-16T08:03:34,819     writing top-level names to /tmp/pip-pip-egg-info-86e5dtew/MDAnalysis.egg-info/top_level.txt
2021-07-16T08:03:34,821     writing manifest file '/tmp/pip-pip-egg-info-86e5dtew/MDAnalysis.egg-info/SOURCES.txt'
2021-07-16T08:03:35,023     reading manifest file '/tmp/pip-pip-egg-info-86e5dtew/MDAnalysis.egg-info/SOURCES.txt'
2021-07-16T08:03:35,026     reading manifest template 'MANIFEST.in'
2021-07-16T08:03:35,257     warning: no files found matching 'MDAnalysis/coordinates/xdrfile/src/*'
2021-07-16T08:03:35,257     warning: no files found matching 'MDAnalysis/lib/src/pyqcprot/*'
2021-07-16T08:03:35,799     warning: no previously-included files matching '*.pyc' found anywhere in distribution
2021-07-16T08:03:35,803     warning: no previously-included files matching '*.pyo' found anywhere in distribution
2021-07-16T08:03:35,806     warning: no previously-included files matching '*.pyd' found anywhere in distribution
2021-07-16T08:03:35,809     warning: no previously-included files matching '*~' found anywhere in distribution
2021-07-16T08:03:35,809     adding license file 'LICENSE'
2021-07-16T08:03:35,809     adding license file 'AUTHORS'
2021-07-16T08:03:35,854     writing manifest file '/tmp/pip-pip-egg-info-86e5dtew/MDAnalysis.egg-info/SOURCES.txt'
2021-07-16T08:03:35,942   Source in /tmp/pip-wheel-g1n8ix0t/mdanalysis_50498136201448a3b5abe4aafa6868ec has version 1.0.0, which satisfies requirement mdanalysis==1.0.0 from https://files.pythonhosted.org/packages/c9/ae/11905971cc6cdb436bff040270f58fb3fc54ef77aea2ce2dfc269129f74e/MDAnalysis-1.0.0.tar.gz#sha256=f45a024aca45e390ff1c45ca90beb2180b78881be377e2a1aa9cd6c109bcfa81
2021-07-16T08:03:35,943   Removed mdanalysis==1.0.0 from https://files.pythonhosted.org/packages/c9/ae/11905971cc6cdb436bff040270f58fb3fc54ef77aea2ce2dfc269129f74e/MDAnalysis-1.0.0.tar.gz#sha256=f45a024aca45e390ff1c45ca90beb2180b78881be377e2a1aa9cd6c109bcfa81 from build tracker '/tmp/pip-req-tracker-mbws08l1'
2021-07-16T08:03:35,949 Created temporary directory: /tmp/pip-unpack-xmqys3zw
2021-07-16T08:03:35,950 Building wheels for collected packages: mdanalysis
2021-07-16T08:03:35,954   Created temporary directory: /tmp/pip-wheel-pouc7zgf
2021-07-16T08:03:35,954   Building wheel for mdanalysis (setup.py): started
2021-07-16T08:03:35,955   Destination directory: /tmp/pip-wheel-pouc7zgf
2021-07-16T08:03:35,955   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-g1n8ix0t/mdanalysis_50498136201448a3b5abe4aafa6868ec/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-g1n8ix0t/mdanalysis_50498136201448a3b5abe4aafa6868ec/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-pouc7zgf
2021-07-16T08:03:37,177   /tmp/pip-wheel-g1n8ix0t/mdanalysis_50498136201448a3b5abe4aafa6868ec/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.
2021-07-16T08:03:37,177     self.config = configparser.SafeConfigParser()
2021-07-16T08:03:37,408   Attempting to autodetect OpenMP support... Compiler supports OpenMP
2021-07-16T08:03:37,409   Will not attempt to use Cython.
2021-07-16T08:03:37,689   running bdist_wheel
2021-07-16T08:03:37,692   The [wheel] section is deprecated. Use [bdist_wheel] instead.
2021-07-16T08:03:37,696   running build
2021-07-16T08:03:37,696   running build_py
2021-07-16T08:03:37,838   creating build
2021-07-16T08:03:37,839   creating build/lib.linux-armv7l-3.9
2021-07-16T08:03:37,839   creating build/lib.linux-armv7l-3.9/MDAnalysis
2021-07-16T08:03:37,840   copying MDAnalysis/units.py -> build/lib.linux-armv7l-3.9/MDAnalysis
2021-07-16T08:03:37,843   copying MDAnalysis/authors.py -> build/lib.linux-armv7l-3.9/MDAnalysis
2021-07-16T08:03:37,844   copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis
2021-07-16T08:03:37,846   copying MDAnalysis/version.py -> build/lib.linux-armv7l-3.9/MDAnalysis
2021-07-16T08:03:37,848   copying MDAnalysis/due.py -> build/lib.linux-armv7l-3.9/MDAnalysis
2021-07-16T08:03:37,850   copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-3.9/MDAnalysis
2021-07-16T08:03:37,852   creating build/lib.linux-armv7l-3.9/MDAnalysis/visualization
2021-07-16T08:03:37,853   copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization
2021-07-16T08:03:37,856   copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization
2021-07-16T08:03:37,858   copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization
2021-07-16T08:03:37,861   creating build/lib.linux-armv7l-3.9/MDAnalysis/transformations
2021-07-16T08:03:37,862   copying MDAnalysis/transformations/wrap.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations
2021-07-16T08:03:37,865   copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations
2021-07-16T08:03:37,867   copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations
2021-07-16T08:03:37,870   copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations
2021-07-16T08:03:37,872   copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations
2021-07-16T08:03:37,874   copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations
2021-07-16T08:03:37,878   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,879   copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,882   copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,884   copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,889   copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,892   copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,895   copying MDAnalysis/analysis/hole.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,898   copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,901   copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,903   copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,907   copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,909   copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,913   copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,915   copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,917   copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,920   copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,923   copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,925   copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,928   copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,930   copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,934   copying MDAnalysis/analysis/helanal.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:03:37,938   creating build/lib.linux-armv7l-3.9/MDAnalysis/selections
2021-07-16T08:03:37,939   copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections
2021-07-16T08:03:37,942   copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections
2021-07-16T08:03:37,944   copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections
2021-07-16T08:03:37,946   copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections
2021-07-16T08:03:37,948   copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections
2021-07-16T08:03:37,950   copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections
2021-07-16T08:03:37,952   copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections
2021-07-16T08:03:37,954   creating build/lib.linux-armv7l-3.9/MDAnalysis/tests
2021-07-16T08:03:37,955   copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-3.9/MDAnalysis/tests
2021-07-16T08:03:37,957   copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/tests
2021-07-16T08:03:37,962   creating build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,963   copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,965   copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,967   copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,971   copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,974   copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,978   copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,980   copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,983   copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,985   copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,988   copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,990   copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,993   copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,995   copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:37,998   copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,002   copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,005   copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,008   copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,011   copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,013   copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,017   copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,019   copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,022   copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,024   copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,027   copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,030   copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,032   copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,034   copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,037   copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,040   copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,042   copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,045   copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates
2021-07-16T08:03:38,048   creating build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary
2021-07-16T08:03:38,049   copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary
2021-07-16T08:03:38,053   copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary
2021-07-16T08:03:38,056   copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary
2021-07-16T08:03:38,058   copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary
2021-07-16T08:03:38,063   creating build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,064   copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,066   copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,068   copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,071   copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,073   copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,075   copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,077   copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,080   copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,082   copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,085   copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,087   copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,089   copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,091   copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,094   copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,097   copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,100   copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,102   copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,104   copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,107   copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,109   copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,112   copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,114   copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,117   copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,119   copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,122   copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,124   copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,127   copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,130   copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology
2021-07-16T08:03:38,134   creating build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,135   copying MDAnalysis/lib/correlations.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,138   copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,141   copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,144   copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,148   copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,149   copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,152   copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,156   copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,159   copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,164   creating build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,165   copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,172   copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,176   copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,179   copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,182   copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,184   copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,187   copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,191   copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core
2021-07-16T08:03:38,196   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds
2021-07-16T08:03:38,196   copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds
2021-07-16T08:03:38,200   copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds
2021-07-16T08:03:38,204   copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds
2021-07-16T08:03:38,206   copying MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds
2021-07-16T08:03:38,212   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data
2021-07-16T08:03:38,213   copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data
2021-07-16T08:03:38,215   copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data
2021-07-16T08:03:38,217   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds
2021-07-16T08:03:38,218   copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds
2021-07-16T08:03:38,221   copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds
2021-07-16T08:03:38,224   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2
2021-07-16T08:03:38,225   copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2
2021-07-16T08:03:38,228   copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2
2021-07-16T08:03:38,232   copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2
2021-07-16T08:03:38,234   copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2
2021-07-16T08:03:38,237   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy
2021-07-16T08:03:38,238   copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy
2021-07-16T08:03:38,240   copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy
2021-07-16T08:03:38,244   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/utils
2021-07-16T08:03:38,244   copying MDAnalysis/analysis/utils/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/utils
2021-07-16T08:03:38,247   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore
2021-07-16T08:03:38,248   copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore
2021-07-16T08:03:38,250   copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore
2021-07-16T08:03:38,255   copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore
2021-07-16T08:03:38,257   copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore
2021-07-16T08:03:38,259   copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore
2021-07-16T08:03:38,262   copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore
2021-07-16T08:03:38,265   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering
2021-07-16T08:03:38,266   copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering
2021-07-16T08:03:38,269   copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering
2021-07-16T08:03:38,271   copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering
2021-07-16T08:03:38,273   copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering
2021-07-16T08:03:38,277   creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction
2021-07-16T08:03:38,278   copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction
2021-07-16T08:03:38,280   copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction
2021-07-16T08:03:38,283   copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction
2021-07-16T08:03:38,285   creating build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr
2021-07-16T08:03:38,286   copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr
2021-07-16T08:03:38,290   copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr
2021-07-16T08:03:38,292   copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr
2021-07-16T08:03:38,295   copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr
2021-07-16T08:03:38,298   creating build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats
2021-07-16T08:03:38,299   copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats
2021-07-16T08:03:38,304   copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data
2021-07-16T08:03:38,309   copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data
2021-07-16T08:03:38,331   running build_ext
2021-07-16T08:03:38,335   building 'MDAnalysis.lib.formats.libdcd' extension
2021-07-16T08:03:38,632   creating build/temp.linux-armv7l-3.9
2021-07-16T08:03:38,632   creating build/temp.linux-armv7l-3.9/MDAnalysis
2021-07-16T08:03:38,633   creating build/temp.linux-armv7l-3.9/MDAnalysis/lib
2021-07-16T08:03:38,634   creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats
2021-07-16T08:03:38,635   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 -fsigned-zeros
2021-07-16T08:03:38,665   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:03:39,023   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:03:39,023                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:03:39,024                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:03:39,024                    from MDAnalysis/lib/formats/libdcd.c:629:
2021-07-16T08:03:39,024   /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]
2021-07-16T08:03:39,024      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:03:39,024         |  ^~~~~~~
2021-07-16T08:03:39,087   In file included from MDAnalysis/lib/formats/libdcd.c:635:
2021-07-16T08:03:39,087   MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’:
2021-07-16T08:03:39,087   MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:03:39,088     562 |       if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
2021-07-16T08:03:39,088         |                     ^~
2021-07-16T08:03:39,090   MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’:
2021-07-16T08:03:39,091   MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable]
2021-07-16T08:03:39,091     698 |   struct tm *tmbuf;
2021-07-16T08:03:39,091         |              ^~~~~
2021-07-16T08:03:39,091   MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable]
2021-07-16T08:03:39,091     697 |   time_t cur_time;
2021-07-16T08:03:39,091         |          ^~~~~~~~
2021-07-16T08:03:40,179   MDAnalysis/lib/formats/libdcd.c: In function ‘__Pyx_decode_c_string’:
2021-07-16T08:03:40,195   MDAnalysis/lib/formats/libdcd.c:31624:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-16T08:03:40,195   31624 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T08:03:40,195         |         ^~~~~~
2021-07-16T08:03:40,195   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T08:03:40,195                    from /usr/include/python3.9/Python.h:97,
2021-07-16T08:03:40,195                    from MDAnalysis/lib/formats/libdcd.c:34:
2021-07-16T08:03:40,196   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T08:03:40,196     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T08:03:40,196         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:03:41,055   In file included from MDAnalysis/lib/formats/include/readdcd.h:25,
2021-07-16T08:03:41,055                    from MDAnalysis/lib/formats/libdcd.c:635:
2021-07-16T08:03:41,055   At top level:
2021-07-16T08:03:41,055   MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function]
2021-07-16T08:03:41,055      96 | static void swap2_aligned(void *v, long ndata) {
2021-07-16T08:03:41,056         |             ^~~~~~~~~~~~~
2021-07-16T08:03:41,056   MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function]
2021-07-16T08:03:41,056      32 | static void swap2_unaligned(void *v, long ndata) {
2021-07-16T08:03:41,056         |             ^~~~~~~~~~~~~~~
2021-07-16T08:03:41,056   In file included from MDAnalysis/lib/formats/libdcd.c:634:
2021-07-16T08:03:41,056   MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function]
2021-07-16T08:03:41,057     453 | static int fio_write_str(fio_fd fd, const char *str) {
2021-07-16T08:03:41,057         |            ^~~~~~~~~~~~~
2021-07-16T08:03:41,057   MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function]
2021-07-16T08:03:41,057     449 | static int fio_read_int32(fio_fd fd, int *i) {
2021-07-16T08:03:41,057         |            ^~~~~~~~~~~~~~
2021-07-16T08:04:13,930   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
2021-07-16T08:04:14,155   building 'MDAnalysis.lib.c_distances' extension
2021-07-16T08:04:14,156   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -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 -fsigned-zeros
2021-07-16T08:04:14,191   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:04:14,547   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:04:14,547                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:04:14,547                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:04:14,547                    from MDAnalysis/lib/c_distances.c:630:
2021-07-16T08:04:14,547   /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]
2021-07-16T08:04:14,548      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:04:14,548         |  ^~~~~~~
2021-07-16T08:04:15,285   MDAnalysis/lib/c_distances.c: In function ‘__Pyx_decode_c_string’:
2021-07-16T08:04:15,297   MDAnalysis/lib/c_distances.c:25095:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-16T08:04:15,297   25095 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T08:04:15,297         |         ^~~~~~
2021-07-16T08:04:15,297   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T08:04:15,298                    from /usr/include/python3.9/Python.h:97,
2021-07-16T08:04:15,298                    from MDAnalysis/lib/c_distances.c:35:
2021-07-16T08:04:15,298   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T08:04:15,298     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T08:04:15,298         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:04:36,923   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
2021-07-16T08:04:37,127   building 'MDAnalysis.lib.c_distances_openmp' extension
2021-07-16T08:04:37,128   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 -fsigned-zeros
2021-07-16T08:04:37,159   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:04:37,506   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:04:37,507                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:04:37,507                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:04:37,507                    from MDAnalysis/lib/c_distances_openmp.c:630:
2021-07-16T08:04:37,507   /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]
2021-07-16T08:04:37,507      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:04:37,507         |  ^~~~~~~
2021-07-16T08:04:42,691   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
2021-07-16T08:04:42,845   building 'MDAnalysis.lib.qcprot' extension
2021-07-16T08:04:42,845   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 -fsigned-zeros
2021-07-16T08:04:42,874   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:04:43,222   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:04:43,222                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:04:43,222                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:04:43,223                    from MDAnalysis/lib/qcprot.c:625:
2021-07-16T08:04:43,223   /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]
2021-07-16T08:04:43,223      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:04:43,223         |  ^~~~~~~
2021-07-16T08:04:43,279   MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’:
2021-07-16T08:04:43,280   MDAnalysis/lib/qcprot.c:2276:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:04:43,280    2276 |     for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) {
2021-07-16T08:04:43,281         |                                     ^
2021-07-16T08:04:43,284   MDAnalysis/lib/qcprot.c:2484:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:04:43,284    2484 |     for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) {
2021-07-16T08:04:43,284         |                                     ^
2021-07-16T08:04:48,678   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
2021-07-16T08:04:48,810   building 'MDAnalysis.lib._transformations' extension
2021-07-16T08:04:48,811   creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/src
2021-07-16T08:04:48,811   creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/src/transformations
2021-07-16T08:04:48,812   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 -fsigned-zeros
2021-07-16T08:04:48,839   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:04:49,182   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:04:49,182                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:04:49,182                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:04:49,182                    from MDAnalysis/lib/src/transformations/transformations.c:73:
2021-07-16T08:04:49,183   /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]
2021-07-16T08:04:49,183      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:04:49,183         |  ^~~~~~~
2021-07-16T08:04:49,248   MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’:
2021-07-16T08:04:49,249   MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,249    1845 |                 #pragma vector always
2021-07-16T08:04:49,249         |
2021-07-16T08:04:49,252   MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,252    1962 |                     #pragma vector always
2021-07-16T08:04:49,252         |
2021-07-16T08:04:49,252   MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,253    1986 |                     #pragma vector always
2021-07-16T08:04:49,253         |
2021-07-16T08:04:49,256   MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’:
2021-07-16T08:04:49,257   MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations]
2021-07-16T08:04:49,257    2122 |     if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) {
2021-07-16T08:04:49,257         |     ^~
2021-07-16T08:04:49,258   In file included from /usr/include/python3.9/Python.h:97,
2021-07-16T08:04:49,258                    from MDAnalysis/lib/src/transformations/transformations.c:68:
2021-07-16T08:04:49,258   /usr/include/python3.9/unicodeobject.h:177:43: note: declared here
2021-07-16T08:04:49,258     177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize(
2021-07-16T08:04:49,258         |                                           ^~~~~~~~~~~~~~~~~
2021-07-16T08:04:49,292   MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’:
2021-07-16T08:04:49,293   MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,293    3427 |             #pragma vector always
2021-07-16T08:04:49,293         |
2021-07-16T08:04:49,295   MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,295    3508 |                 #pragma vector always
2021-07-16T08:04:49,295         |
2021-07-16T08:04:49,300   MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’:
2021-07-16T08:04:49,301   MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,301    3610 |             #pragma vector always
2021-07-16T08:04:49,301         |
2021-07-16T08:04:49,301   MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,301    3615 |             #pragma vector always
2021-07-16T08:04:49,301         |
2021-07-16T08:04:49,306   MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,306    3679 |                 #pragma vector always
2021-07-16T08:04:49,306         |
2021-07-16T08:04:49,307   MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas]
2021-07-16T08:04:49,307    3684 |                 #pragma vector always
2021-07-16T08:04:49,307         |
2021-07-16T08:04:49,376   At top level:
2021-07-16T08:04:49,376   MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function]
2021-07-16T08:04:49,376     910 | PyConverter_DoubleVector4Copy(
2021-07-16T08:04:49,376         | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:04:49,376   MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function]
2021-07-16T08:04:49,377     804 | PyConverter_DoubleArrayOrNone(
2021-07-16T08:04:49,377         | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:04:49,377   MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function]
2021-07-16T08:04:49,377     774 | PyConverter_DoubleArray(
2021-07-16T08:04:49,377         | ^~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:04:55,116   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
2021-07-16T08:04:55,252   building 'MDAnalysis.lib.formats.libmdaxdr' extension
2021-07-16T08:04:55,253   creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src
2021-07-16T08:04:55,254   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 -fsigned-zeros
2021-07-16T08:04:55,286   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:04:55,627   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:04:55,627                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:04:55,627                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:04:55,627                    from MDAnalysis/lib/formats/libmdaxdr.c:651:
2021-07-16T08:04:55,628   /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]
2021-07-16T08:04:55,628      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:04:55,628         |  ^~~~~~~
2021-07-16T08:04:55,659   In file included from MDAnalysis/lib/formats/libmdaxdr.c:654:
2021-07-16T08:04:55,660   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:04:55,660       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:04:55,660         |
2021-07-16T08:04:55,661   In file included from MDAnalysis/lib/formats/libmdaxdr.c:655:
2021-07-16T08:04:55,661   MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:04:55,661       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:04:55,661         |
2021-07-16T08:04:55,662   In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43,
2021-07-16T08:04:55,662                    from MDAnalysis/lib/formats/libmdaxdr.c:655:
2021-07-16T08:04:55,662   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:04:55,662       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:04:55,662         |
2021-07-16T08:04:55,663   In file included from MDAnalysis/lib/formats/libmdaxdr.c:656:
2021-07-16T08:04:55,663   MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:04:55,663       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:04:55,663         |
2021-07-16T08:04:56,519   MDAnalysis/lib/formats/libmdaxdr.c: In function ‘__Pyx_decode_c_string’:
2021-07-16T08:04:56,534   MDAnalysis/lib/formats/libmdaxdr.c:30016:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-16T08:04:56,534   30016 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T08:04:56,534         |         ^~~~~~
2021-07-16T08:04:56,535   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T08:04:56,535                    from /usr/include/python3.9/Python.h:97,
2021-07-16T08:04:56,535                    from MDAnalysis/lib/formats/libmdaxdr.c:56:
2021-07-16T08:04:56,535   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T08:04:56,535     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T08:04:56,535         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:05:26,231   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 -fsigned-zeros
2021-07-16T08:05:26,261   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:05:26,330   In file included from MDAnalysis/lib/formats/src/trr_seek.c:30:
2021-07-16T08:05:26,330   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:26,330       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:26,330         |
2021-07-16T08:05:26,335   In file included from MDAnalysis/lib/formats/src/trr_seek.c:31:
2021-07-16T08:05:26,335   MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:26,335       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:26,335         |
2021-07-16T08:05:26,335   In file included from MDAnalysis/lib/formats/include/xdrfile_trr.h:42,
2021-07-16T08:05:26,336                    from MDAnalysis/lib/formats/src/trr_seek.c:31:
2021-07-16T08:05:26,336   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:26,336       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:26,336         |
2021-07-16T08:05:26,338   MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’:
2021-07-16T08:05:26,339   MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable]
2021-07-16T08:05:26,339      39 |   int result, framebytes, totalframebytes;
2021-07-16T08:05:26,339         |                           ^~~~~~~~~~~~~~~
2021-07-16T08:05:26,339   MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable]
2021-07-16T08:05:26,340      38 |   float time, lambda;
2021-07-16T08:05:26,340         |               ^~~~~~
2021-07-16T08:05:26,340   MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable]
2021-07-16T08:05:26,340      38 |   float time, lambda;
2021-07-16T08:05:26,340         |         ^~~~
2021-07-16T08:05:26,453   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 -fsigned-zeros
2021-07-16T08:05:26,478   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:05:26,598   In file included from MDAnalysis/lib/formats/src/xdrfile.c:62:
2021-07-16T08:05:26,599   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:26,599       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:26,599         |
2021-07-16T08:05:26,609   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’:
2021-07-16T08:05:26,609   MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:05:26,609     501 |     while (size >= num && num_of_bits < 32)
2021-07-16T08:05:26,610         |                 ^~
2021-07-16T08:05:26,610   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’:
2021-07-16T08:05:26,611   MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,611     547 |     while (bytes[num_of_bytes] >= num)
2021-07-16T08:05:26,611         |                                ^~
2021-07-16T08:05:26,613   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’:
2021-07-16T08:05:26,613   MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:05:26,614     656 |     if (num_of_bits >= num_of_bytes * 8)
2021-07-16T08:05:26,614         |                     ^~
2021-07-16T08:05:26,614   MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:05:26,614     658 |   for (i = 0; i < num_of_bytes; i++)
2021-07-16T08:05:26,615         |                 ^
2021-07-16T08:05:26,615   MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:05:26,615     666 |   for (i = 0; i < num_of_bytes-1; i++)
2021-07-16T08:05:26,615         |                 ^
2021-07-16T08:05:26,616   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’:
2021-07-16T08:05:26,617   MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,617     706 |   if (lastbits < num_of_bits)
2021-07-16T08:05:26,617         |                ^
2021-07-16T08:05:26,619   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’:
2021-07-16T08:05:26,620   MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,620     816 |  if(size3>xfp->buf1size)
2021-07-16T08:05:26,620         |          ^
2021-07-16T08:05:26,622   MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,622     868 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-16T08:05:26,622         |                   ^
2021-07-16T08:05:26,623   MDAnalysis/lib/formats/src/xdrfile.c:868:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-16T08:05:26,623     868 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-16T08:05:26,623         |                                     ^~~
2021-07-16T08:05:26,626   MDAnalysis/lib/formats/src/xdrfile.c:794:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-16T08:05:26,626     794 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-16T08:05:26,626         |                         ^~~~~~
2021-07-16T08:05:26,626   MDAnalysis/lib/formats/src/xdrfile.c:791:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-16T08:05:26,626     791 |  int smallidx, minidx, maxidx;
2021-07-16T08:05:26,626         |                ^~~~~~
2021-07-16T08:05:26,627   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
2021-07-16T08:05:26,627   MDAnalysis/lib/formats/src/xdrfile.c:1012:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,627    1012 |  if(size3>xfp->buf1size)
2021-07-16T08:05:26,628         |          ^
2021-07-16T08:05:26,633   MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:05:26,633    1135 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
2021-07-16T08:05:26,633         |                  ^
2021-07-16T08:05:26,633   MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,633    1141 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-16T08:05:26,634         |                   ^
2021-07-16T08:05:26,634   MDAnalysis/lib/formats/src/xdrfile.c:1141:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-16T08:05:26,634    1141 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-16T08:05:26,634         |                                     ^~~
2021-07-16T08:05:26,638   MDAnalysis/lib/formats/src/xdrfile.c:1273:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:05:26,638    1273 |  if(tmp==(unsigned int)buf2[0])
2021-07-16T08:05:26,638         |        ^~
2021-07-16T08:05:26,638   MDAnalysis/lib/formats/src/xdrfile.c:1001:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-16T08:05:26,638    1001 |  int errval=1;
2021-07-16T08:05:26,639         |      ^~~~~~
2021-07-16T08:05:26,639   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_double’:
2021-07-16T08:05:26,640   MDAnalysis/lib/formats/src/xdrfile.c:1313:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,640    1313 |  if(size3>xfp->buf1size)
2021-07-16T08:05:26,641         |          ^
2021-07-16T08:05:26,643   MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,643    1368 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-16T08:05:26,643         |                   ^
2021-07-16T08:05:26,644   MDAnalysis/lib/formats/src/xdrfile.c:1368:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-16T08:05:26,644    1368 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-16T08:05:26,644         |                                     ^~~
2021-07-16T08:05:26,647   MDAnalysis/lib/formats/src/xdrfile.c:1290:25: warning: variable ‘larger’ set but not used [-Wunused-but-set-variable]
2021-07-16T08:05:26,647    1290 |  int smallnum, smaller, larger, i, is_smaller, run;
2021-07-16T08:05:26,647         |                         ^~~~~~
2021-07-16T08:05:26,648   MDAnalysis/lib/formats/src/xdrfile.c:1287:16: warning: variable ‘minidx’ set but not used [-Wunused-but-set-variable]
2021-07-16T08:05:26,648    1287 |  int smallidx, minidx, maxidx;
2021-07-16T08:05:26,648         |                ^~~~~~
2021-07-16T08:05:26,649   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
2021-07-16T08:05:26,650   MDAnalysis/lib/formats/src/xdrfile.c:1504:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,650    1504 |  if(size3>xfp->buf1size) {
2021-07-16T08:05:26,650         |          ^
2021-07-16T08:05:26,658   MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:05:26,658    1619 |  while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
2021-07-16T08:05:26,659         |                  ^
2021-07-16T08:05:26,659   MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-16T08:05:26,659    1624 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-16T08:05:26,660         |                   ^
2021-07-16T08:05:26,661   MDAnalysis/lib/formats/src/xdrfile.c:1624:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2021-07-16T08:05:26,661    1624 |  maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
2021-07-16T08:05:26,661         |                                     ^~~
2021-07-16T08:05:26,665   MDAnalysis/lib/formats/src/xdrfile.c:1734:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-16T08:05:26,665    1734 |  if(tmp==(unsigned int)buf2[0])
2021-07-16T08:05:26,665         |        ^~
2021-07-16T08:05:26,666   MDAnalysis/lib/formats/src/xdrfile.c:1494:6: warning: variable ‘errval’ set but not used [-Wunused-but-set-variable]
2021-07-16T08:05:26,666    1494 |  int errval=1;
2021-07-16T08:05:26,666         |      ^~~~~~
2021-07-16T08:05:26,682   MDAnalysis/lib/formats/src/xdrfile.c: At top level:
2021-07-16T08:05:26,683   MDAnalysis/lib/formats/src/xdrfile.c:2535:3: warning: initialization of ‘unsigned int (*)(XDR *)’ from incompatible pointer type ‘int64_t (*)(XDR *)’ {aka ‘long long int (*)(XDR *)’} [-Wincompatible-pointer-types]
2021-07-16T08:05:26,683    2535 |   xdrstdio_getpos,  /* get offset in the stream */
2021-07-16T08:05:26,683         |   ^~~~~~~~~~~~~~~
2021-07-16T08:05:26,683   MDAnalysis/lib/formats/src/xdrfile.c:2535:3: note: (near initialization for ‘xdrstdio_ops.x_getpostn’)
2021-07-16T08:05:26,684   MDAnalysis/lib/formats/src/xdrfile.c:2536:3: warning: initialization of ‘int (*)(XDR *, unsigned int)’ from incompatible pointer type ‘int (*)(XDR *, int64_t,  int)’ {aka ‘int (*)(XDR *, long long int,  int)’} [-Wincompatible-pointer-types]
2021-07-16T08:05:26,685    2536 |   xdrstdio_setpos,  /* set offset in the stream */
2021-07-16T08:05:26,685         |   ^~~~~~~~~~~~~~~
2021-07-16T08:05:26,685   MDAnalysis/lib/formats/src/xdrfile.c:2536:3: note: (near initialization for ‘xdrstdio_ops.x_setpostn’)
2021-07-16T08:05:28,330   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_write_string’:
2021-07-16T08:05:28,331   MDAnalysis/lib/formats/src/xdrfile.c:2361:5: warning: ‘size’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T08:05:28,331    2361 |  if (size > maxsize)
2021-07-16T08:05:28,331         |     ^
2021-07-16T08:05:28,333   MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here
2021-07-16T08:05:28,333    2335 |  unsigned int size;
2021-07-16T08:05:28,333         |               ^~~~
2021-07-16T08:05:28,767   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’:
2021-07-16T08:05:28,768   MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T08:05:28,768    1157 |    abs(thiscoord[2] - prevcoord[2]) < larger) {
2021-07-16T08:05:28,768         |        ~~~~~~~~~~~~~^~~~~~~~~~~~~~
2021-07-16T08:05:28,769   MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T08:05:28,769    1156 |    abs(thiscoord[1] - prevcoord[1]) < larger &&
2021-07-16T08:05:28,769         |        ~~~~~~~~~~~~~^~~~~~~~~~~~~~
2021-07-16T08:05:28,769   MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T08:05:28,770    1155 |    abs(thiscoord[0] - prevcoord[0]) < larger &&
2021-07-16T08:05:28,770         |        ~~~~~~~~~~~~~^~~~~~~~~~~~~~
2021-07-16T08:05:29,525   MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’:
2021-07-16T08:05:29,526   MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T08:05:29,527    1639 |    abs(thiscoord[2] - prevcoord[2]) < larger) {
2021-07-16T08:05:29,527         |        ~~~~~~~~~~~~~^~~~~~~~~~~~~~
2021-07-16T08:05:29,527   MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T08:05:29,528    1638 |    abs(thiscoord[1] - prevcoord[1]) < larger &&
2021-07-16T08:05:29,528         |        ~~~~~~~~~~~~~^~~~~~~~~~~~~~
2021-07-16T08:05:29,529   MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
2021-07-16T08:05:29,529    1637 |    abs(thiscoord[0] - prevcoord[0]) < larger &&
2021-07-16T08:05:29,529         |        ~~~~~~~~~~~~~^~~~~~~~~~~~~~
2021-07-16T08:05:30,561   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 -fsigned-zeros
2021-07-16T08:05:30,586   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:05:30,654   In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38:
2021-07-16T08:05:30,654   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:30,654       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:30,654         |
2021-07-16T08:05:30,659   In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39:
2021-07-16T08:05:30,659   MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:30,659       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:30,659         |
2021-07-16T08:05:30,659   In file included from MDAnalysis/lib/formats/include/xdrfile_trr.h:42,
2021-07-16T08:05:30,660                    from MDAnalysis/lib/formats/src/xdrfile_trr.c:39:
2021-07-16T08:05:30,660   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:30,660       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:30,660         |
2021-07-16T08:05:30,661   MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’:
2021-07-16T08:05:30,661   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]
2021-07-16T08:05:30,661      78 |     if (slen != strlen(version) + 1)
2021-07-16T08:05:30,662         |              ^~
2021-07-16T08:05:30,662   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]
2021-07-16T08:05:30,662      86 |     if (xdrfile_write_string(version, xd) != (strlen(version) + 1))
2021-07-16T08:05:30,662         |                                           ^~
2021-07-16T08:05:30,679   MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’:
2021-07-16T08:05:30,679   MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized]
2021-07-16T08:05:30,679     408 |   return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder);
2021-07-16T08:05:30,679         |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:05:31,773   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 -fsigned-zeros
2021-07-16T08:05:31,796   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:05:31,827   In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30:
2021-07-16T08:05:31,827   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:31,827       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:31,827         |
2021-07-16T08:05:31,840   In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31:
2021-07-16T08:05:31,840   MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:31,840       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:31,840         |
2021-07-16T08:05:31,841   In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43,
2021-07-16T08:05:31,841                    from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31:
2021-07-16T08:05:31,841   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:31,841       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:31,841         |
2021-07-16T08:05:31,975   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 -fsigned-zeros
2021-07-16T08:05:32,001   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:05:32,028   In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25:
2021-07-16T08:05:32,029   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:32,029       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:32,029         |
2021-07-16T08:05:32,040   In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26:
2021-07-16T08:05:32,040   MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:32,040       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:32,040         |
2021-07-16T08:05:32,040   In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43,
2021-07-16T08:05:32,040                    from MDAnalysis/lib/formats/src/xtc_seek.c:26:
2021-07-16T08:05:32,041   MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
2021-07-16T08:05:32,041       5 |  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
2021-07-16T08:05:32,041         |
2021-07-16T08:05:32,209   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
2021-07-16T08:05:32,448   building 'MDAnalysis.lib.formats.cython_util' extension
2021-07-16T08:05:32,449   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 -fsigned-zeros
2021-07-16T08:05:32,477   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:05:32,829   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:05:32,829                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:05:32,829                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:05:32,829                    from MDAnalysis/lib/formats/cython_util.c:625:
2021-07-16T08:05:32,829   /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]
2021-07-16T08:05:32,830      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:05:32,830         |  ^~~~~~~
2021-07-16T08:05:33,441   MDAnalysis/lib/formats/cython_util.c: In function ‘__Pyx_decode_c_string’:
2021-07-16T08:05:33,455   MDAnalysis/lib/formats/cython_util.c:21699:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations]
2021-07-16T08:05:33,456   21699 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T08:05:33,456         |         ^~~~~~
2021-07-16T08:05:33,456   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T08:05:33,456                    from /usr/include/python3.9/Python.h:97,
2021-07-16T08:05:33,456                    from MDAnalysis/lib/formats/cython_util.c:30:
2021-07-16T08:05:33,456   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T08:05:33,457     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T08:05:33,457         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:05:49,776   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
2021-07-16T08:05:49,941   building 'MDAnalysis.analysis.encore.cutils' extension
2021-07-16T08:05:49,942   creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis
2021-07-16T08:05:49,942   creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore
2021-07-16T08:05:49,943   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 -fsigned-zeros
2021-07-16T08:05:49,971   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:05:50,317   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:05:50,317                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:05:50,317                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:05:50,317                    from MDAnalysis/analysis/encore/cutils.c:625:
2021-07-16T08:05:50,317   /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]
2021-07-16T08:05:50,318      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:05:50,318         |  ^~~~~~~
2021-07-16T08:05:52,479   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
2021-07-16T08:05:52,598   building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension
2021-07-16T08:05:52,599   creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering
2021-07-16T08:05:52,600   creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/src
2021-07-16T08:05:52,600   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 -fsigned-zeros
2021-07-16T08:05:52,629   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:05:52,981   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:05:52,981                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:05:52,981                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:05:52,981                    from MDAnalysis/analysis/encore/clustering/affinityprop.c:631:
2021-07-16T08:05:52,981   /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]
2021-07-16T08:05:52,982      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:05:52,982         |  ^~~~~~~
2021-07-16T08:06:02,900   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 -fsigned-zeros
2021-07-16T08:06:02,928   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:06:03,963   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
2021-07-16T08:06:04,105   building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension
2021-07-16T08:06:04,105   creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction
2021-07-16T08:06:04,106   creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/src
2021-07-16T08:06:04,106   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 -fsigned-zeros
2021-07-16T08:06:04,135   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:06:04,841   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 -fsigned-zeros
2021-07-16T08:06:04,867   cc1: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:06:05,215   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:06:05,216                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:06:05,216                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:06:05,216                    from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:631:
2021-07-16T08:06:05,216   /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]
2021-07-16T08:06:05,216      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:06:05,216         |  ^~~~~~~
2021-07-16T08:06:09,104   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
2021-07-16T08:06:09,246   building 'MDAnalysis.lib._cutil' extension
2021-07-16T08:06:09,246   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 -fsigned-zeros -std=c++11
2021-07-16T08:06:09,281   cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:06:09,537   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:06:09,538                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:06:09,538                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:06:09,538                    from MDAnalysis/lib/_cutil.cpp:645:
2021-07-16T08:06:09,538   /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]
2021-07-16T08:06:09,538      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:06:09,539         |  ^~~~~~~
2021-07-16T08:06:11,572   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*))’:
2021-07-16T08:06:11,572   MDAnalysis/lib/_cutil.cpp:25449:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations]
2021-07-16T08:06:11,572   25449 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T08:06:11,572         |                                             ^
2021-07-16T08:06:11,572   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T08:06:11,573                    from /usr/include/python3.9/Python.h:97,
2021-07-16T08:06:11,573                    from MDAnalysis/lib/_cutil.cpp:36:
2021-07-16T08:06:11,573   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T08:06:11,573     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T08:06:11,573         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,339   In file included from MDAnalysis/lib/_cutil.cpp:667:
2021-07-16T08:06:12,339   MDAnalysis/lib/include/calc_distances.h: At global scope:
2021-07-16T08:06:12,339   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]
2021-07-16T08:06:12,339     833 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,339         |             ^~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,340   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]
2021-07-16T08:06:12,340     797 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,340         |             ^~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,340   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]
2021-07-16T08:06:12,340     769 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,340         |             ^~~~~~~~~~~~~~
2021-07-16T08:06:12,341   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]
2021-07-16T08:06:12,341     692 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,341         |             ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,341   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]
2021-07-16T08:06:12,341     649 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,341         |             ^~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,342   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]
2021-07-16T08:06:12,342     618 | static void _calc_angle(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,342         |             ^~~~~~~~~~~
2021-07-16T08:06:12,342   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]
2021-07-16T08:06:12,342     593 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,343         |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,343   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]
2021-07-16T08:06:12,343     568 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,343         |             ^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,343   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]
2021-07-16T08:06:12,343     549 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2,
2021-07-16T08:06:12,343         |             ^~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,344   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]
2021-07-16T08:06:12,344     494 | static void _calc_self_distance_array_triclinic(coordinate* ref, int numref,
2021-07-16T08:06:12,344         |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,344   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]
2021-07-16T08:06:12,344     461 | static void _calc_self_distance_array_ortho(coordinate* ref, int numref,
2021-07-16T08:06:12,344         |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,344   MDAnalysis/lib/include/calc_distances.h:434:13: warning: ‘void _calc_self_distance_array(float (*)[3], int, double*)’ defined but not used [-Wunused-function]
2021-07-16T08:06:12,345     434 | static void _calc_self_distance_array(coordinate* ref, int numref,
2021-07-16T08:06:12,345         |             ^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,345   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]
2021-07-16T08:06:12,345     407 | static void _calc_distance_array_triclinic(coordinate* ref, int numref,
2021-07-16T08:06:12,345         |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,345   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]
2021-07-16T08:06:12,345     380 | static void _calc_distance_array_ortho(coordinate* ref, int numref, coordinate* conf,
2021-07-16T08:06:12,345         |             ^~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,346   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]
2021-07-16T08:06:12,346     359 | static void _calc_distance_array(coordinate* ref, int numref, coordinate* conf,
2021-07-16T08:06:12,346         |             ^~~~~~~~~~~~~~~~~~~~
2021-07-16T08:06:12,346   MDAnalysis/lib/include/calc_distances.h:90:13: warning: ‘void _ortho_pbc(float (*)[3], int, float*)’ defined but not used [-Wunused-function]
2021-07-16T08:06:12,346      90 | static void _ortho_pbc(coordinate* coords, int numcoords, float* box)
2021-07-16T08:06:12,346         |             ^~~~~~~~~~
2021-07-16T08:06:38,296   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
2021-07-16T08:06:38,658   building 'MDAnalysis.lib._augment' extension
2021-07-16T08:06:38,659   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 -fsigned-zeros -std=c++11
2021-07-16T08:06:38,693   cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:06:38,952   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:06:38,952                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:06:38,952                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:06:38,952                    from MDAnalysis/lib/_augment.cpp:640:
2021-07-16T08:06:38,952   /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]
2021-07-16T08:06:38,953      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:06:38,953         |  ^~~~~~~
2021-07-16T08:06:40,633   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*))’:
2021-07-16T08:06:40,633   MDAnalysis/lib/_augment.cpp:24484:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations]
2021-07-16T08:06:40,633   24484 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T08:06:40,633         |                                             ^
2021-07-16T08:06:40,633   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T08:06:40,634                    from /usr/include/python3.9/Python.h:97,
2021-07-16T08:06:40,634                    from MDAnalysis/lib/_augment.cpp:31:
2021-07-16T08:06:40,634   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T08:06:40,634     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T08:06:40,634         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:07:04,613   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
2021-07-16T08:07:04,954   building 'MDAnalysis.lib.nsgrid' extension
2021-07-16T08:07:04,955   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 -fsigned-zeros -std=c++11
2021-07-16T08:07:04,989   cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence
2021-07-16T08:07:05,333   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T08:07:05,333                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T08:07:05,333                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T08:07:05,334                    from MDAnalysis/lib/nsgrid.cpp:646:
2021-07-16T08:07:05,334   /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]
2021-07-16T08:07:05,334      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T08:07:05,334         |  ^~~~~~~
2021-07-16T08:07:07,201   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*))’:
2021-07-16T08:07:07,201   MDAnalysis/lib/nsgrid.cpp:31003:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations]
2021-07-16T08:07:07,201   31003 |         return PyUnicode_FromUnicode(NULL, 0);
2021-07-16T08:07:07,201         |                                             ^
2021-07-16T08:07:07,202   In file included from /usr/include/python3.9/unicodeobject.h:1026,
2021-07-16T08:07:07,202                    from /usr/include/python3.9/Python.h:97,
2021-07-16T08:07:07,203                    from MDAnalysis/lib/nsgrid.cpp:31:
2021-07-16T08:07:07,203   /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here
2021-07-16T08:07:07,203     551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
2021-07-16T08:07:07,203         |                                          ^~~~~~~~~~~~~~~~~~~~~
2021-07-16T08:07:31,557   In file included from /usr/include/c++/10/vector:72,
2021-07-16T08:07:31,557                    from MDAnalysis/lib/nsgrid.cpp:643:
2021-07-16T08:07:31,558   /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<double>]’:
2021-07-16T08:07:31,558   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
2021-07-16T08:07:31,558     426 |       vector<_Tp, _Alloc>::
2021-07-16T08:07:31,558         |       ^~~~~~~~~~~~~~~~~~~
2021-07-16T08:07:31,594   In file included from /usr/include/c++/10/vector:67,
2021-07-16T08:07:31,594                    from MDAnalysis/lib/nsgrid.cpp:643:
2021-07-16T08:07:31,595   /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)’:
2021-07-16T08:07:31,595   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2021-07-16T08:07:31,595    1198 |    _M_realloc_insert(end(), __x);
2021-07-16T08:07:31,595         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-16T08:07:32,654   /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*)’:
2021-07-16T08:07:32,654   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2021-07-16T08:07:32,654    1198 |    _M_realloc_insert(end(), __x);
2021-07-16T08:07:32,654         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-16T08:07:38,312   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
2021-07-16T08:07:38,711   installing to build/bdist.linux-armv7l/wheel
2021-07-16T08:07:38,712   running install
2021-07-16T08:07:38,713   running install_lib
2021-07-16T08:07:38,718   creating build/bdist.linux-armv7l
2021-07-16T08:07:38,719   creating build/bdist.linux-armv7l/wheel
2021-07-16T08:07:38,721   creating build/bdist.linux-armv7l/wheel/MDAnalysis
2021-07-16T08:07:38,723   creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization
2021-07-16T08:07:38,724   copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization
2021-07-16T08:07:38,728   copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization
2021-07-16T08:07:38,730   copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization
2021-07-16T08:07:38,734   creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations
2021-07-16T08:07:38,735   copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/wrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations
2021-07-16T08:07:38,737   copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations
2021-07-16T08:07:38,740   copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations
2021-07-16T08:07:38,742   copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations
2021-07-16T08:07:38,744   copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations
2021-07-16T08:07:38,747   copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations
2021-07-16T08:07:38,750   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,751   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,754   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,757   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,762   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,765   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,768   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,771   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,775   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,778   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds
2021-07-16T08:07:38,779   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds
2021-07-16T08:07:38,782   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds
2021-07-16T08:07:38,786   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds
2021-07-16T08:07:38,788   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds
2021-07-16T08:07:38,793   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data
2021-07-16T08:07:38,794   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data
2021-07-16T08:07:38,798   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data
2021-07-16T08:07:38,800   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data
2021-07-16T08:07:38,801   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data
2021-07-16T08:07:38,805   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds
2021-07-16T08:07:38,806   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds
2021-07-16T08:07:38,809   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds
2021-07-16T08:07:38,812   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2
2021-07-16T08:07:38,813   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2
2021-07-16T08:07:38,816   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2
2021-07-16T08:07:38,819   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2
2021-07-16T08:07:38,821   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2
2021-07-16T08:07:38,823   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,827   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,829   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,833   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy
2021-07-16T08:07:38,834   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy
2021-07-16T08:07:38,836   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy
2021-07-16T08:07:38,839   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,841   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,844   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,846   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,850   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/utils
2021-07-16T08:07:38,850   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/utils/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/utils
2021-07-16T08:07:38,853   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore
2021-07-16T08:07:38,854   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore
2021-07-16T08:07:38,857   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
2021-07-16T08:07:38,863   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore
2021-07-16T08:07:38,867   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore
2021-07-16T08:07:38,869   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore
2021-07-16T08:07:38,872   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering
2021-07-16T08:07:38,873   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering
2021-07-16T08:07:38,876   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
2021-07-16T08:07:38,892   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering
2021-07-16T08:07:38,895   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering
2021-07-16T08:07:38,897   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering
2021-07-16T08:07:38,900   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore
2021-07-16T08:07:38,903   creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction
2021-07-16T08:07:38,904   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction
2021-07-16T08:07:38,907   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
2021-07-16T08:07:38,909   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction
2021-07-16T08:07:38,912   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
2021-07-16T08:07:38,920   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore
2021-07-16T08:07:38,923   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,926   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,929   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,931   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,935   copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/helanal.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis
2021-07-16T08:07:38,939   copying build/lib.linux-armv7l-3.9/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis
2021-07-16T08:07:38,943   creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections
2021-07-16T08:07:38,944   copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections
2021-07-16T08:07:38,947   copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections
2021-07-16T08:07:38,949   copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections
2021-07-16T08:07:38,951   copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections
2021-07-16T08:07:38,953   copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections
2021-07-16T08:07:38,956   copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections
2021-07-16T08:07:38,958   copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections
2021-07-16T08:07:38,961   creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests
2021-07-16T08:07:38,962   copying build/lib.linux-armv7l-3.9/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests
2021-07-16T08:07:38,964   copying build/lib.linux-armv7l-3.9/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests
2021-07-16T08:07:38,967   creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,968   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,971   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,974   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,977   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,980   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,984   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,987   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,990   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,992   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,995   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:38,998   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,001   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,003   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,007   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,010   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,013   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,016   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,019   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,022   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,026   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,028   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,031   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,034   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,037   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,040   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,042   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,045   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,048   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,051   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,053   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,056   copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates
2021-07-16T08:07:39,059   copying build/lib.linux-armv7l-3.9/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis
2021-07-16T08:07:39,061   copying build/lib.linux-armv7l-3.9/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis
2021-07-16T08:07:39,064   copying build/lib.linux-armv7l-3.9/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis
2021-07-16T08:07:39,067   creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary
2021-07-16T08:07:39,068   copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary
2021-07-16T08:07:39,072   copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary
2021-07-16T08:07:39,075   copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary
2021-07-16T08:07:39,077   copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary
2021-07-16T08:07:39,081   creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,083   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,085   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,088   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,090   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,093   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,096   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,099   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,102   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,104   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,107   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,110   creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr
2021-07-16T08:07:39,111   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr
2021-07-16T08:07:39,114   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr
2021-07-16T08:07:39,117   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr
2021-07-16T08:07:39,119   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr
2021-07-16T08:07:39,122   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,124   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,127   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,130   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,133   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,136   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,138   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,141   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,144   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,147   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,150   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,153   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,156   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,158   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,162   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,164   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,167   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,170   copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology
2021-07-16T08:07:39,174   creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,175   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/correlations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,178   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
2021-07-16T08:07:39,188   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,191   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,201   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,203   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,208   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,210   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,262   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,265   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,269   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,272   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,306   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,335   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,389   creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats
2021-07-16T08:07:39,390   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
2021-07-16T08:07:39,412   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
2021-07-16T08:07:39,458   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
2021-07-16T08:07:39,505   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats
2021-07-16T08:07:39,507   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,511   copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib
2021-07-16T08:07:39,521   copying build/lib.linux-armv7l-3.9/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis
2021-07-16T08:07:39,523   copying build/lib.linux-armv7l-3.9/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis
2021-07-16T08:07:39,525   creating build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,526   copying build/lib.linux-armv7l-3.9/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,532   copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,535   copying build/lib.linux-armv7l-3.9/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,537   copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,540   copying build/lib.linux-armv7l-3.9/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,542   copying build/lib.linux-armv7l-3.9/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,545   copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,549   copying build/lib.linux-armv7l-3.9/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core
2021-07-16T08:07:39,553   running install_egg_info
2021-07-16T08:07:39,581   running egg_info
2021-07-16T08:07:39,583   writing MDAnalysis.egg-info/PKG-INFO
2021-07-16T08:07:39,585   writing dependency_links to MDAnalysis.egg-info/dependency_links.txt
2021-07-16T08:07:39,587   writing requirements to MDAnalysis.egg-info/requires.txt
2021-07-16T08:07:39,588   writing top-level names to MDAnalysis.egg-info/top_level.txt
2021-07-16T08:07:39,669   reading manifest file 'MDAnalysis.egg-info/SOURCES.txt'
2021-07-16T08:07:39,878   reading manifest template 'MANIFEST.in'
2021-07-16T08:07:40,120   warning: no files found matching 'MDAnalysis/coordinates/xdrfile/src/*'
2021-07-16T08:07:40,120   warning: no files found matching 'MDAnalysis/lib/src/pyqcprot/*'
2021-07-16T08:07:40,610   warning: no previously-included files matching '*.pyc' found anywhere in distribution
2021-07-16T08:07:40,615   warning: no previously-included files matching '*.pyo' found anywhere in distribution
2021-07-16T08:07:40,621   warning: no previously-included files matching '*.pyd' found anywhere in distribution
2021-07-16T08:07:40,627   warning: no previously-included files matching '*~' found anywhere in distribution
2021-07-16T08:07:40,627   adding license file 'LICENSE'
2021-07-16T08:07:40,627   adding license file 'AUTHORS'
2021-07-16T08:07:40,691   writing manifest file 'MDAnalysis.egg-info/SOURCES.txt'
2021-07-16T08:07:40,695   Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-1.0.0-py3.9.egg-info
2021-07-16T08:07:40,710   running install_scripts
2021-07-16T08:07:40,814   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2021-07-16T08:07:40,815   adding license file "AUTHORS" (matched pattern "AUTHORS*")
2021-07-16T08:07:40,822   creating build/bdist.linux-armv7l/wheel/MDAnalysis-1.0.0.dist-info/WHEEL
2021-07-16T08:07:40,824   creating '/tmp/pip-wheel-pouc7zgf/MDAnalysis-1.0.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-16T08:07:40,827   adding 'MDAnalysis/__init__.py'
2021-07-16T08:07:40,829   adding 'MDAnalysis/authors.py'
2021-07-16T08:07:40,830   adding 'MDAnalysis/due.py'
2021-07-16T08:07:40,832   adding 'MDAnalysis/exceptions.py'
2021-07-16T08:07:40,834   adding 'MDAnalysis/units.py'
2021-07-16T08:07:40,836   adding 'MDAnalysis/version.py'
2021-07-16T08:07:40,838   adding 'MDAnalysis/analysis/__init__.py'
2021-07-16T08:07:40,846   adding 'MDAnalysis/analysis/align.py'
2021-07-16T08:07:40,849   adding 'MDAnalysis/analysis/base.py'
2021-07-16T08:07:40,851   adding 'MDAnalysis/analysis/contacts.py'
2021-07-16T08:07:40,860   adding 'MDAnalysis/analysis/density.py'
2021-07-16T08:07:40,863   adding 'MDAnalysis/analysis/diffusionmap.py'
2021-07-16T08:07:40,866   adding 'MDAnalysis/analysis/dihedrals.py'
2021-07-16T08:07:40,868   adding 'MDAnalysis/analysis/distances.py'
2021-07-16T08:07:40,870   adding 'MDAnalysis/analysis/gnm.py'
2021-07-16T08:07:40,874   adding 'MDAnalysis/analysis/helanal.py'
2021-07-16T08:07:40,882   adding 'MDAnalysis/analysis/hole.py'
2021-07-16T08:07:40,885   adding 'MDAnalysis/analysis/leaflet.py'
2021-07-16T08:07:40,886   adding 'MDAnalysis/analysis/lineardensity.py'
2021-07-16T08:07:40,889   adding 'MDAnalysis/analysis/nuclinfo.py'
2021-07-16T08:07:40,892   adding 'MDAnalysis/analysis/pca.py'
2021-07-16T08:07:40,894   adding 'MDAnalysis/analysis/polymer.py'
2021-07-16T08:07:40,904   adding 'MDAnalysis/analysis/psa.py'
2021-07-16T08:07:40,907   adding 'MDAnalysis/analysis/rdf.py'
2021-07-16T08:07:40,911   adding 'MDAnalysis/analysis/rms.py'
2021-07-16T08:07:40,917   adding 'MDAnalysis/analysis/waterdynamics.py'
2021-07-16T08:07:40,918   adding 'MDAnalysis/analysis/data/__init__.py'
2021-07-16T08:07:40,920   adding 'MDAnalysis/analysis/data/filenames.py'
2021-07-16T08:07:40,923   adding 'MDAnalysis/analysis/data/janin_ref_data.npy'
2021-07-16T08:07:40,929   adding 'MDAnalysis/analysis/data/rama_ref_data.npy'
2021-07-16T08:07:40,931   adding 'MDAnalysis/analysis/encore/__init__.py'
2021-07-16T08:07:40,932   adding 'MDAnalysis/analysis/encore/bootstrap.py'
2021-07-16T08:07:40,934   adding 'MDAnalysis/analysis/encore/confdistmatrix.py'
2021-07-16T08:07:40,936   adding 'MDAnalysis/analysis/encore/covariance.py'
2021-07-16T08:07:40,965   adding 'MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:40,972   adding 'MDAnalysis/analysis/encore/similarity.py'
2021-07-16T08:07:40,975   adding 'MDAnalysis/analysis/encore/utils.py'
2021-07-16T08:07:40,977   adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py'
2021-07-16T08:07:40,979   adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py'
2021-07-16T08:07:40,980   adding 'MDAnalysis/analysis/encore/clustering/__init__.py'
2021-07-16T08:07:41,080   adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:41,085   adding 'MDAnalysis/analysis/encore/clustering/cluster.py'
2021-07-16T08:07:41,087   adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py'
2021-07-16T08:07:41,088   adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py'
2021-07-16T08:07:41,090   adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py'
2021-07-16T08:07:41,148   adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:41,152   adding 'MDAnalysis/analysis/hbonds/__init__.py'
2021-07-16T08:07:41,160   adding 'MDAnalysis/analysis/hbonds/hbond_analysis.py'
2021-07-16T08:07:41,163   adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py'
2021-07-16T08:07:41,172   adding 'MDAnalysis/analysis/hbonds/wbridge_analysis.py'
2021-07-16T08:07:41,174   adding 'MDAnalysis/analysis/hole2/__init__.py'
2021-07-16T08:07:41,180   adding 'MDAnalysis/analysis/hole2/hole.py'
2021-07-16T08:07:41,182   adding 'MDAnalysis/analysis/hole2/templates.py'
2021-07-16T08:07:41,185   adding 'MDAnalysis/analysis/hole2/utils.py'
2021-07-16T08:07:41,186   adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py'
2021-07-16T08:07:41,189   adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py'
2021-07-16T08:07:41,191   adding 'MDAnalysis/analysis/legacy/__init__.py'
2021-07-16T08:07:41,195   adding 'MDAnalysis/analysis/legacy/x3dna.py'
2021-07-16T08:07:41,196   adding 'MDAnalysis/analysis/utils/__init__.py'
2021-07-16T08:07:41,199   adding 'MDAnalysis/auxiliary/XVG.py'
2021-07-16T08:07:41,202   adding 'MDAnalysis/auxiliary/__init__.py'
2021-07-16T08:07:41,207   adding 'MDAnalysis/auxiliary/base.py'
2021-07-16T08:07:41,208   adding 'MDAnalysis/auxiliary/core.py'
2021-07-16T08:07:41,211   adding 'MDAnalysis/coordinates/CRD.py'
2021-07-16T08:07:41,213   adding 'MDAnalysis/coordinates/DCD.py'
2021-07-16T08:07:41,216   adding 'MDAnalysis/coordinates/DLPoly.py'
2021-07-16T08:07:41,217   adding 'MDAnalysis/coordinates/DMS.py'
2021-07-16T08:07:41,219   adding 'MDAnalysis/coordinates/FHIAIMS.py'
2021-07-16T08:07:41,221   adding 'MDAnalysis/coordinates/GMS.py'
2021-07-16T08:07:41,224   adding 'MDAnalysis/coordinates/GRO.py'
2021-07-16T08:07:41,225   adding 'MDAnalysis/coordinates/GSD.py'
2021-07-16T08:07:41,227   adding 'MDAnalysis/coordinates/INPCRD.py'
2021-07-16T08:07:41,230   adding 'MDAnalysis/coordinates/LAMMPS.py'
2021-07-16T08:07:41,231   adding 'MDAnalysis/coordinates/MMTF.py'
2021-07-16T08:07:41,234   adding 'MDAnalysis/coordinates/MOL2.py'
2021-07-16T08:07:41,236   adding 'MDAnalysis/coordinates/NAMDBIN.py'
2021-07-16T08:07:41,242   adding 'MDAnalysis/coordinates/PDB.py'
2021-07-16T08:07:41,245   adding 'MDAnalysis/coordinates/PDBQT.py'
2021-07-16T08:07:41,247   adding 'MDAnalysis/coordinates/PQR.py'
2021-07-16T08:07:41,249   adding 'MDAnalysis/coordinates/ParmEd.py'
2021-07-16T08:07:41,255   adding 'MDAnalysis/coordinates/TRJ.py'
2021-07-16T08:07:41,257   adding 'MDAnalysis/coordinates/TRR.py'
2021-07-16T08:07:41,259   adding 'MDAnalysis/coordinates/TRZ.py'
2021-07-16T08:07:41,261   adding 'MDAnalysis/coordinates/TXYZ.py'
2021-07-16T08:07:41,263   adding 'MDAnalysis/coordinates/XDR.py'
2021-07-16T08:07:41,265   adding 'MDAnalysis/coordinates/XTC.py'
2021-07-16T08:07:41,267   adding 'MDAnalysis/coordinates/XYZ.py'
2021-07-16T08:07:41,271   adding 'MDAnalysis/coordinates/__init__.py'
2021-07-16T08:07:41,281   adding 'MDAnalysis/coordinates/base.py'
2021-07-16T08:07:41,285   adding 'MDAnalysis/coordinates/chain.py'
2021-07-16T08:07:41,288   adding 'MDAnalysis/coordinates/chemfiles.py'
2021-07-16T08:07:41,289   adding 'MDAnalysis/coordinates/core.py'
2021-07-16T08:07:41,292   adding 'MDAnalysis/coordinates/memory.py'
2021-07-16T08:07:41,294   adding 'MDAnalysis/coordinates/null.py'
2021-07-16T08:07:41,295   adding 'MDAnalysis/core/__init__.py'
2021-07-16T08:07:41,297   adding 'MDAnalysis/core/_get_readers.py'
2021-07-16T08:07:41,316   adding 'MDAnalysis/core/groups.py'
2021-07-16T08:07:41,322   adding 'MDAnalysis/core/selection.py'
2021-07-16T08:07:41,325   adding 'MDAnalysis/core/topology.py'
2021-07-16T08:07:41,332   adding 'MDAnalysis/core/topologyattrs.py'
2021-07-16T08:07:41,337   adding 'MDAnalysis/core/topologyobjects.py'
2021-07-16T08:07:41,344   adding 'MDAnalysis/core/universe.py'
2021-07-16T08:07:41,346   adding 'MDAnalysis/lib/NeighborSearch.py'
2021-07-16T08:07:41,348   adding 'MDAnalysis/lib/__init__.py'
2021-07-16T08:07:41,611   adding 'MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:41,948   adding 'MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:42,015   adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:42,263   adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:42,326   adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:42,331   adding 'MDAnalysis/lib/correlations.py'
2021-07-16T08:07:42,336   adding 'MDAnalysis/lib/distances.py'
2021-07-16T08:07:42,338   adding 'MDAnalysis/lib/log.py'
2021-07-16T08:07:42,341   adding 'MDAnalysis/lib/mdamath.py'
2021-07-16T08:07:42,726   adding 'MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:42,745   adding 'MDAnalysis/lib/pkdtree.py'
2021-07-16T08:07:42,812   adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:42,822   adding 'MDAnalysis/lib/transformations.py'
2021-07-16T08:07:42,833   adding 'MDAnalysis/lib/util.py'
2021-07-16T08:07:42,835   adding 'MDAnalysis/lib/formats/__init__.py'
2021-07-16T08:07:43,038   adding 'MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:43,437   adding 'MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:43,851   adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T08:07:43,869   adding 'MDAnalysis/selections/__init__.py'
2021-07-16T08:07:43,871   adding 'MDAnalysis/selections/base.py'
2021-07-16T08:07:43,872   adding 'MDAnalysis/selections/charmm.py'
2021-07-16T08:07:43,874   adding 'MDAnalysis/selections/gromacs.py'
2021-07-16T08:07:43,875   adding 'MDAnalysis/selections/jmol.py'
2021-07-16T08:07:43,877   adding 'MDAnalysis/selections/pymol.py'
2021-07-16T08:07:43,878   adding 'MDAnalysis/selections/vmd.py'
2021-07-16T08:07:43,880   adding 'MDAnalysis/tests/__init__.py'
2021-07-16T08:07:43,881   adding 'MDAnalysis/tests/datafiles.py'
2021-07-16T08:07:43,883   adding 'MDAnalysis/topology/CRDParser.py'
2021-07-16T08:07:43,885   adding 'MDAnalysis/topology/DLPolyParser.py'
2021-07-16T08:07:43,887   adding 'MDAnalysis/topology/DMSParser.py'
2021-07-16T08:07:43,888   adding 'MDAnalysis/topology/ExtendedPDBParser.py'
2021-07-16T08:07:43,890   adding 'MDAnalysis/topology/FHIAIMSParser.py'
2021-07-16T08:07:43,891   adding 'MDAnalysis/topology/GMSParser.py'
2021-07-16T08:07:43,893   adding 'MDAnalysis/topology/GROParser.py'
2021-07-16T08:07:43,895   adding 'MDAnalysis/topology/GSDParser.py'
2021-07-16T08:07:43,897   adding 'MDAnalysis/topology/HoomdXMLParser.py'
2021-07-16T08:07:43,900   adding 'MDAnalysis/topology/ITPParser.py'
2021-07-16T08:07:43,903   adding 'MDAnalysis/topology/LAMMPSParser.py'
2021-07-16T08:07:43,905   adding 'MDAnalysis/topology/MMTFParser.py'
2021-07-16T08:07:43,907   adding 'MDAnalysis/topology/MOL2Parser.py'
2021-07-16T08:07:43,909   adding 'MDAnalysis/topology/MinimalParser.py'
2021-07-16T08:07:43,911   adding 'MDAnalysis/topology/PDBParser.py'
2021-07-16T08:07:43,913   adding 'MDAnalysis/topology/PDBQTParser.py'
2021-07-16T08:07:43,915   adding 'MDAnalysis/topology/PQRParser.py'
2021-07-16T08:07:43,918   adding 'MDAnalysis/topology/PSFParser.py'
2021-07-16T08:07:43,920   adding 'MDAnalysis/topology/ParmEdParser.py'
2021-07-16T08:07:43,923   adding 'MDAnalysis/topology/TOPParser.py'
2021-07-16T08:07:43,925   adding 'MDAnalysis/topology/TPRParser.py'
2021-07-16T08:07:43,927   adding 'MDAnalysis/topology/TXYZParser.py'
2021-07-16T08:07:43,929   adding 'MDAnalysis/topology/XYZParser.py'
2021-07-16T08:07:43,931   adding 'MDAnalysis/topology/__init__.py'
2021-07-16T08:07:43,933   adding 'MDAnalysis/topology/base.py'
2021-07-16T08:07:43,935   adding 'MDAnalysis/topology/core.py'
2021-07-16T08:07:43,937   adding 'MDAnalysis/topology/guessers.py'
2021-07-16T08:07:43,939   adding 'MDAnalysis/topology/tables.py'
2021-07-16T08:07:43,941   adding 'MDAnalysis/topology/tpr/__init__.py'
2021-07-16T08:07:43,943   adding 'MDAnalysis/topology/tpr/obj.py'
2021-07-16T08:07:43,945   adding 'MDAnalysis/topology/tpr/setting.py'
2021-07-16T08:07:43,950   adding 'MDAnalysis/topology/tpr/utils.py'
2021-07-16T08:07:43,952   adding 'MDAnalysis/transformations/__init__.py'
2021-07-16T08:07:43,954   adding 'MDAnalysis/transformations/fit.py'
2021-07-16T08:07:43,956   adding 'MDAnalysis/transformations/positionaveraging.py'
2021-07-16T08:07:43,958   adding 'MDAnalysis/transformations/rotate.py'
2021-07-16T08:07:43,960   adding 'MDAnalysis/transformations/translate.py'
2021-07-16T08:07:43,961   adding 'MDAnalysis/transformations/wrap.py'
2021-07-16T08:07:43,963   adding 'MDAnalysis/visualization/__init__.py'
2021-07-16T08:07:43,966   adding 'MDAnalysis/visualization/streamlines.py'
2021-07-16T08:07:43,969   adding 'MDAnalysis/visualization/streamlines_3D.py'
2021-07-16T08:07:43,972   adding 'MDAnalysis-1.0.0.dist-info/AUTHORS'
2021-07-16T08:07:43,976   adding 'MDAnalysis-1.0.0.dist-info/LICENSE'
2021-07-16T08:07:43,978   adding 'MDAnalysis-1.0.0.dist-info/METADATA'
2021-07-16T08:07:43,979   adding 'MDAnalysis-1.0.0.dist-info/WHEEL'
2021-07-16T08:07:43,980   adding 'MDAnalysis-1.0.0.dist-info/top_level.txt'
2021-07-16T08:07:43,983   adding 'MDAnalysis-1.0.0.dist-info/RECORD'
2021-07-16T08:07:44,071   removing build/bdist.linux-armv7l/wheel
2021-07-16T08:07:44,268   Building wheel for mdanalysis (setup.py): finished with status 'done'
2021-07-16T08:07:44,340   Created wheel for mdanalysis: filename=MDAnalysis-1.0.0-cp39-cp39-linux_armv7l.whl size=5699207 sha256=e43dbbd4ecd06fb475d80e5dae571708415e1287e6dd2c669c98095e13ea2ae8
2021-07-16T08:07:44,341   Stored in directory: /tmp/pip-ephem-wheel-cache-4x8_fxvz/wheels/50/9f/9e/803a0fafc253694711c79fb2940e717d32cf5114719a444cc5
2021-07-16T08:07:44,360 Successfully built mdanalysis
2021-07-16T08:07:44,543 Removed build tracker: '/tmp/pip-req-tracker-mbws08l1'