2021-07-29T19:39:27,398 Created temporary directory: /tmp/pip-ephem-wheel-cache-p8_kbzny 2021-07-29T19:39:27,401 Created temporary directory: /tmp/pip-req-tracker-bq_o6689 2021-07-29T19:39:27,402 Initialized build tracking at /tmp/pip-req-tracker-bq_o6689 2021-07-29T19:39:27,402 Created build tracker: /tmp/pip-req-tracker-bq_o6689 2021-07-29T19:39:27,402 Entered build tracker: /tmp/pip-req-tracker-bq_o6689 2021-07-29T19:39:27,403 Created temporary directory: /tmp/pip-wheel-9jkjktma 2021-07-29T19:39:27,441 WARNING: The index url "/" seems invalid, please provide a scheme. 2021-07-29T19:39:27,441 WARNING: The index url "t" seems invalid, please provide a scheme. 2021-07-29T19:39:27,442 WARNING: The index url "m" seems invalid, please provide a scheme. 2021-07-29T19:39:27,442 WARNING: The index url "p" seems invalid, please provide a scheme. 2021-07-29T19:39:27,442 Looking in indexes: https://pypi.org/simple, /, t, m, p 2021-07-29T19:39:27,445 WARNING: Location '/mdanalysis/' is ignored: 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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) 2021-07-29T19:39:27,661 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 2021-07-29T19:39:27,662 Skipping link: not a file: https://pypi.org/simple/mdanalysis/ 2021-07-29T19:39:27,684 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates 2021-07-29T19:39:27,702 Collecting mdanalysis==2.0.0b0 2021-07-29T19:39:27,703 Created temporary directory: /tmp/pip-unpack-n70pzjko 2021-07-29T19:39:27,747 Downloading MDAnalysis-2.0.0b0.tar.gz (3.4 MB) 2021-07-29T19:39:29,665 Added mdanalysis==2.0.0b0 from https://files.pythonhosted.org/packages/55/d1/9e302a51bdf6b3d0b7045c20b42203ad8ad20bf2103e8c19db2da868c6e7/MDAnalysis-2.0.0b0.tar.gz#sha256=09e0b855bddca9c386d3d674e3baf684ebcbb1668348844372232dc2b9a4ea4e to build tracker '/tmp/pip-req-tracker-bq_o6689' 2021-07-29T19:39:29,666 Running setup.py (path:/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/setup.py) egg_info for package mdanalysis 2021-07-29T19:39:29,667 Created temporary directory: /tmp/pip-pip-egg-info-bcbbi_md 2021-07-29T19:39:29,667 Running command python setup.py egg_info 2021-07-29T19:40:32,519 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-29T19:40:32,520 Will attempt to use Cython. 2021-07-29T19:40:32,520 Compiling MDAnalysis/lib/formats/libdcd.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,520 Compiling MDAnalysis/lib/c_distances.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,520 Compiling MDAnalysis/lib/c_distances_openmp.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,520 Compiling MDAnalysis/lib/qcprot.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,521 Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,521 Compiling MDAnalysis/lib/formats/cython_util.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,521 Compiling MDAnalysis/analysis/encore/cutils.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,521 Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,521 Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-29T19:40:32,521 Compiling MDAnalysis/lib/_cutil.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-29T19:40:32,521 Compiling MDAnalysis/lib/_augment.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-29T19:40:32,521 Compiling MDAnalysis/lib/nsgrid.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libcpp/vector.pxd. 2021-07-29T19:40:32,522 [ 1/12] Cythonizing MDAnalysis/lib/_augment.pyx 2021-07-29T19:40:32,522 [ 2/12] Cythonizing MDAnalysis/lib/_cutil.pyx 2021-07-29T19:40:32,522 [ 3/12] Cythonizing MDAnalysis/lib/nsgrid.pyx 2021-07-29T19:40:32,522 [ 4/12] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx 2021-07-29T19:40:32,522 [ 5/12] Cythonizing MDAnalysis/analysis/encore/cutils.pyx 2021-07-29T19:40:32,522 [ 6/12] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx 2021-07-29T19:40:32,522 [ 7/12] Cythonizing MDAnalysis/lib/c_distances.pyx 2021-07-29T19:40:32,522 [ 8/12] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx 2021-07-29T19:40:32,523 [ 9/12] Cythonizing MDAnalysis/lib/formats/cython_util.pyx 2021-07-29T19:40:32,523 [10/12] Cythonizing MDAnalysis/lib/formats/libdcd.pyx 2021-07-29T19:40:32,523 [11/12] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx 2021-07-29T19:40:32,523 [12/12] Cythonizing MDAnalysis/lib/qcprot.pyx 2021-07-29T19:40:32,769 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0.0-beta' to '2.0.0b0' 2021-07-29T19:40:32,769 warnings.warn(tmpl.format(**locals())) 2021-07-29T19:40:33,070 running egg_info 2021-07-29T19:40:33,073 creating /tmp/pip-pip-egg-info-bcbbi_md/MDAnalysis.egg-info 2021-07-29T19:40:33,074 writing /tmp/pip-pip-egg-info-bcbbi_md/MDAnalysis.egg-info/PKG-INFO 2021-07-29T19:40:33,077 writing dependency_links to /tmp/pip-pip-egg-info-bcbbi_md/MDAnalysis.egg-info/dependency_links.txt 2021-07-29T19:40:33,080 writing requirements to /tmp/pip-pip-egg-info-bcbbi_md/MDAnalysis.egg-info/requires.txt 2021-07-29T19:40:33,081 writing top-level names to /tmp/pip-pip-egg-info-bcbbi_md/MDAnalysis.egg-info/top_level.txt 2021-07-29T19:40:33,083 writing manifest file '/tmp/pip-pip-egg-info-bcbbi_md/MDAnalysis.egg-info/SOURCES.txt' 2021-07-29T19:40:33,263 reading manifest file '/tmp/pip-pip-egg-info-bcbbi_md/MDAnalysis.egg-info/SOURCES.txt' 2021-07-29T19:40:33,265 reading manifest template 'MANIFEST.in' 2021-07-29T19:40:33,445 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2021-07-29T19:40:33,448 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-29T19:40:33,450 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2021-07-29T19:40:33,451 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2021-07-29T19:40:33,453 warning: no previously-included files matching '*~' found anywhere in distribution 2021-07-29T19:40:33,455 warning: no previously-included files matching '.git' found anywhere in distribution 2021-07-29T19:40:33,455 adding license file 'LICENSE' 2021-07-29T19:40:33,455 adding license file 'AUTHORS' 2021-07-29T19:40:33,473 writing manifest file '/tmp/pip-pip-egg-info-bcbbi_md/MDAnalysis.egg-info/SOURCES.txt' 2021-07-29T19:40:33,952 Source in /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7 has version 2.0.0b0, which satisfies requirement mdanalysis==2.0.0b0 from https://files.pythonhosted.org/packages/55/d1/9e302a51bdf6b3d0b7045c20b42203ad8ad20bf2103e8c19db2da868c6e7/MDAnalysis-2.0.0b0.tar.gz#sha256=09e0b855bddca9c386d3d674e3baf684ebcbb1668348844372232dc2b9a4ea4e 2021-07-29T19:40:33,953 Removed mdanalysis==2.0.0b0 from https://files.pythonhosted.org/packages/55/d1/9e302a51bdf6b3d0b7045c20b42203ad8ad20bf2103e8c19db2da868c6e7/MDAnalysis-2.0.0b0.tar.gz#sha256=09e0b855bddca9c386d3d674e3baf684ebcbb1668348844372232dc2b9a4ea4e from build tracker '/tmp/pip-req-tracker-bq_o6689' 2021-07-29T19:40:33,957 Created temporary directory: /tmp/pip-unpack-ebcsuxvn 2021-07-29T19:40:33,958 Building wheels for collected packages: mdanalysis 2021-07-29T19:40:33,962 Created temporary directory: /tmp/pip-wheel-a4qrqsvq 2021-07-29T19:40:33,962 Building wheel for mdanalysis (setup.py): started 2021-07-29T19:40:33,963 Destination directory: /tmp/pip-wheel-a4qrqsvq 2021-07-29T19:40:33,963 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/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-a4qrqsvq 2021-07-29T19:40:35,092 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-29T19:40:35,093 Will attempt to use Cython. 2021-07-29T19:40:36,228 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:484: UserWarning: Normalizing '2.0.0-beta' to '2.0.0b0' 2021-07-29T19:40:36,228 warnings.warn(tmpl.format(**locals())) 2021-07-29T19:40:36,297 running bdist_wheel 2021-07-29T19:40:36,300 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2021-07-29T19:40:36,302 running build 2021-07-29T19:40:36,302 running build_py 2021-07-29T19:40:36,440 creating build 2021-07-29T19:40:36,440 creating build/lib.linux-armv7l-3.9 2021-07-29T19:40:36,441 creating build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-29T19:40:36,443 copying MDAnalysis/due.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-29T19:40:36,445 copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-29T19:40:36,448 copying MDAnalysis/authors.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-29T19:40:36,449 copying MDAnalysis/units.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-29T19:40:36,452 copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-29T19:40:36,454 copying MDAnalysis/version.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-29T19:40:36,457 creating build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-29T19:40:36,458 copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-29T19:40:36,460 copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-29T19:40:36,463 copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-29T19:40:36,465 copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary 2021-07-29T19:40:36,470 creating build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,471 copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,473 copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,475 copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,477 copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,480 copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,482 copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,484 copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,486 copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,488 copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,490 copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,493 copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,495 copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,498 copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,501 copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,503 copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,506 copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,509 copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,511 copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,513 copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,515 copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,518 copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,521 copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,523 copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,525 copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,528 copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,530 copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,532 copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,534 copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-29T19:40:36,538 creating build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-29T19:40:36,539 copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-29T19:40:36,541 copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-29T19:40:36,542 copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-29T19:40:36,544 copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-29T19:40:36,546 copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-29T19:40:36,548 copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-29T19:40:36,550 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-29T19:40:36,553 creating build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,554 copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,556 copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,558 copying MDAnalysis/transformations/wrap.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,560 copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,563 copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,564 copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,567 copying MDAnalysis/transformations/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,569 copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-3.9/MDAnalysis/transformations 2021-07-29T19:40:36,572 creating build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,573 copying MDAnalysis/core/accessors.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,575 copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,578 copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,582 copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,584 copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,588 copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,593 copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,595 copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,598 copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-29T19:40:36,606 creating build/lib.linux-armv7l-3.9/MDAnalysis/converters 2021-07-29T19:40:36,606 copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/converters 2021-07-29T19:40:36,609 copying MDAnalysis/converters/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/converters 2021-07-29T19:40:36,610 copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/converters 2021-07-29T19:40:36,613 copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-armv7l-3.9/MDAnalysis/converters 2021-07-29T19:40:36,615 copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/converters 2021-07-29T19:40:36,617 copying MDAnalysis/converters/RDKit.py -> build/lib.linux-armv7l-3.9/MDAnalysis/converters 2021-07-29T19:40:36,620 copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-armv7l-3.9/MDAnalysis/converters 2021-07-29T19:40:36,622 creating build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-29T19:40:36,623 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-29T19:40:36,626 copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-29T19:40:36,628 copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-29T19:40:36,631 creating build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-29T19:40:36,632 copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-29T19:40:36,634 copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-29T19:40:36,638 creating build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,639 copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,641 copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,644 copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,646 copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,649 copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,652 copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,655 copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,657 copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,659 copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,663 copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,665 copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,668 copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,671 copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,676 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,678 copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,682 copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,684 copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,686 copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,690 copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,692 copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,694 copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,697 copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,699 copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,702 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,704 copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,707 copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,708 copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,713 copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,716 copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,719 copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,721 copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,723 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-29T19:40:36,727 creating build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,728 copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,730 copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,732 copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,736 copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,739 copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,742 copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,744 copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,749 copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,751 copying MDAnalysis/lib/correlations.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,753 copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,757 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,758 copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,761 copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,764 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,766 copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,768 copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,771 copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,774 copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,778 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,780 copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,782 copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,785 copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,788 copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,793 copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,795 copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,799 copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,801 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,803 copying MDAnalysis/analysis/msd.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,806 copying MDAnalysis/analysis/bat.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,809 copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,811 copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,814 copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:40:36,817 creating build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-29T19:40:36,817 copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-29T19:40:36,819 copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-29T19:40:36,821 copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-29T19:40:36,825 copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-29T19:40:36,828 creating build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats 2021-07-29T19:40:36,829 copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats 2021-07-29T19:40:36,831 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-29T19:40:36,832 copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-29T19:40:36,834 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-29T19:40:36,836 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:40:36,837 copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:40:36,840 copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:40:36,842 copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:40:36,845 copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:40:36,850 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-29T19:40:36,851 copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-29T19:40:36,855 copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-29T19:40:36,857 copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-29T19:40:36,859 copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-29T19:40:36,861 copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-29T19:40:36,864 copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-29T19:40:36,867 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-29T19:40:36,867 copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-29T19:40:36,869 copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-29T19:40:36,872 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2 2021-07-29T19:40:36,873 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2 2021-07-29T19:40:36,875 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2 2021-07-29T19:40:36,877 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2 2021-07-29T19:40:36,879 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2 2021-07-29T19:40:36,884 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy 2021-07-29T19:40:36,884 copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy 2021-07-29T19:40:36,886 copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy 2021-07-29T19:40:36,890 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-29T19:40:36,891 copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-29T19:40:36,893 copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-29T19:40:36,896 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-29T19:40:36,898 copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-29T19:40:36,901 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-29T19:40:36,902 copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-29T19:40:36,904 copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-29T19:40:36,907 copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-29T19:40:36,911 copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-29T19:40:36,914 copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data 2021-07-29T19:40:36,938 running build_ext 2021-07-29T19:40:36,941 building 'MDAnalysis.lib.formats.libdcd' extension 2021-07-29T19:40:36,941 creating build/temp.linux-armv7l-3.9 2021-07-29T19:40:36,942 creating build/temp.linux-armv7l-3.9/MDAnalysis 2021-07-29T19:40:36,942 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib 2021-07-29T19:40:36,943 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats 2021-07-29T19:40:36,943 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/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:40:36,976 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:40:37,420 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:40:37,420 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:40:37,420 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:40:37,420 from MDAnalysis/lib/formats/libdcd.c:653: 2021-07-29T19:40:37,420 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:40:37,420 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:40:37,421 | ^~~~~~~ 2021-07-29T19:40:37,517 In file included from MDAnalysis/lib/formats/libdcd.c:665: 2021-07-29T19:40:37,517 MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’: 2021-07-29T19:40:37,518 MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-29T19:40:37,518 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-29T19:40:37,518 | ^~ 2021-07-29T19:40:37,522 MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’: 2021-07-29T19:40:37,523 MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable] 2021-07-29T19:40:37,523 698 | struct tm *tmbuf; 2021-07-29T19:40:37,523 | ^~~~~ 2021-07-29T19:40:37,523 MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable] 2021-07-29T19:40:37,524 697 | time_t cur_time; 2021-07-29T19:40:37,524 | ^~~~~~~~ 2021-07-29T19:40:39,377 In file included from MDAnalysis/lib/formats/include/readdcd.h:25, 2021-07-29T19:40:39,377 from MDAnalysis/lib/formats/libdcd.c:665: 2021-07-29T19:40:39,377 At top level: 2021-07-29T19:40:39,377 MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2021-07-29T19:40:39,378 96 | static void swap2_aligned(void *v, long ndata) { 2021-07-29T19:40:39,378 | ^~~~~~~~~~~~~ 2021-07-29T19:40:39,378 MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2021-07-29T19:40:39,378 32 | static void swap2_unaligned(void *v, long ndata) { 2021-07-29T19:40:39,378 | ^~~~~~~~~~~~~~~ 2021-07-29T19:40:39,378 In file included from MDAnalysis/lib/formats/libdcd.c:664: 2021-07-29T19:40:39,379 MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-29T19:40:39,379 453 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-29T19:40:39,379 | ^~~~~~~~~~~~~ 2021-07-29T19:40:39,379 MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-29T19:40:39,379 449 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-29T19:40:39,379 | ^~~~~~~~~~~~~~ 2021-07-29T19:41:12,282 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 2021-07-29T19:41:12,510 building 'MDAnalysis.lib.c_distances' extension 2021-07-29T19:41:12,510 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:41:12,542 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:41:12,900 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:41:12,900 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:41:12,900 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:41:12,900 from MDAnalysis/lib/c_distances.c:654: 2021-07-29T19:41:12,900 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:41:12,900 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:41:12,900 | ^~~~~~~ 2021-07-29T19:41:35,394 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 2021-07-29T19:41:35,601 building 'MDAnalysis.lib.c_distances_openmp' extension 2021-07-29T19:41:35,601 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:41:35,633 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:41:35,986 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:41:35,987 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:41:35,987 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:41:35,987 from MDAnalysis/lib/c_distances_openmp.c:665: 2021-07-29T19:41:35,987 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:41:35,987 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:41:35,987 | ^~~~~~~ 2021-07-29T19:41:41,113 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 2021-07-29T19:41:41,295 building 'MDAnalysis.lib.qcprot' extension 2021-07-29T19:41:41,295 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/usr/local/lib/python3.9/dist-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 2021-07-29T19:41:41,325 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:41:41,675 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:41:41,676 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:41:41,676 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:41:41,676 from MDAnalysis/lib/qcprot.c:649: 2021-07-29T19:41:41,676 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:41:41,676 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:41:41,677 | ^~~~~~~ 2021-07-29T19:41:41,737 MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’: 2021-07-29T19:41:41,738 MDAnalysis/lib/qcprot.c:2249:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:41:41,738 2249 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2021-07-29T19:41:41,738 | ^ 2021-07-29T19:41:41,741 MDAnalysis/lib/qcprot.c:2457:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:41:41,741 2457 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2021-07-29T19:41:41,741 | ^ 2021-07-29T19:41:47,099 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 2021-07-29T19:41:47,238 building 'MDAnalysis.lib._transformations' extension 2021-07-29T19:41:47,238 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/src 2021-07-29T19:41:47,239 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/src/transformations 2021-07-29T19:41:47,239 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/usr/local/lib/python3.9/dist-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 2021-07-29T19:41:47,270 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:41:47,623 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:41:47,623 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:41:47,624 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:41:47,624 from MDAnalysis/lib/src/transformations/transformations.c:73: 2021-07-29T19:41:47,624 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:41:47,624 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:41:47,624 | ^~~~~~~ 2021-07-29T19:41:47,692 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: 2021-07-29T19:41:47,693 MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,693 1845 | #pragma vector always 2021-07-29T19:41:47,693 | 2021-07-29T19:41:47,697 MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,697 1962 | #pragma vector always 2021-07-29T19:41:47,698 | 2021-07-29T19:41:47,698 MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,699 1986 | #pragma vector always 2021-07-29T19:41:47,699 | 2021-07-29T19:41:47,702 MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: 2021-07-29T19:41:47,704 MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] 2021-07-29T19:41:47,704 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { 2021-07-29T19:41:47,704 | ^~ 2021-07-29T19:41:47,705 In file included from /usr/include/python3.9/Python.h:97, 2021-07-29T19:41:47,705 from MDAnalysis/lib/src/transformations/transformations.c:68: 2021-07-29T19:41:47,705 /usr/include/python3.9/unicodeobject.h:177:43: note: declared here 2021-07-29T19:41:47,705 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( 2021-07-29T19:41:47,705 | ^~~~~~~~~~~~~~~~~ 2021-07-29T19:41:47,740 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: 2021-07-29T19:41:47,741 MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,741 3427 | #pragma vector always 2021-07-29T19:41:47,741 | 2021-07-29T19:41:47,744 MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,744 3508 | #pragma vector always 2021-07-29T19:41:47,744 | 2021-07-29T19:41:47,750 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: 2021-07-29T19:41:47,751 MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,751 3610 | #pragma vector always 2021-07-29T19:41:47,751 | 2021-07-29T19:41:47,752 MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,752 3615 | #pragma vector always 2021-07-29T19:41:47,752 | 2021-07-29T19:41:47,757 MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,757 3679 | #pragma vector always 2021-07-29T19:41:47,757 | 2021-07-29T19:41:47,758 MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-29T19:41:47,758 3684 | #pragma vector always 2021-07-29T19:41:47,759 | 2021-07-29T19:41:47,828 At top level: 2021-07-29T19:41:47,829 MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] 2021-07-29T19:41:47,829 910 | PyConverter_DoubleVector4Copy( 2021-07-29T19:41:47,829 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:41:47,830 MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] 2021-07-29T19:41:47,830 804 | PyConverter_DoubleArrayOrNone( 2021-07-29T19:41:47,830 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:41:47,831 MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] 2021-07-29T19:41:47,831 774 | PyConverter_DoubleArray( 2021-07-29T19:41:47,831 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:41:53,600 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 2021-07-29T19:41:53,744 building 'MDAnalysis.lib.formats.libmdaxdr' extension 2021-07-29T19:41:53,745 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/formats/src 2021-07-29T19:41:53,745 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/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:41:53,780 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:41:54,140 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:41:54,141 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:41:54,141 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:41:54,141 from MDAnalysis/lib/formats/libmdaxdr.c:676: 2021-07-29T19:41:54,141 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:41:54,141 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:41:54,141 | ^~~~~~~ 2021-07-29T19:41:54,181 In file included from MDAnalysis/lib/formats/libmdaxdr.c:685: 2021-07-29T19:41:54,181 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:41:54,182 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:41:54,182 | 2021-07-29T19:41:54,184 In file included from MDAnalysis/lib/formats/libmdaxdr.c:686: 2021-07-29T19:41:54,184 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:41:54,184 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:41:54,184 | 2021-07-29T19:41:54,185 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2021-07-29T19:41:54,185 from MDAnalysis/lib/formats/libmdaxdr.c:686: 2021-07-29T19:41:54,185 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:41:54,185 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:41:54,185 | 2021-07-29T19:41:54,187 In file included from MDAnalysis/lib/formats/libmdaxdr.c:687: 2021-07-29T19:41:54,187 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:41:54,188 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:41:54,188 | 2021-07-29T19:42:25,624 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/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:42:25,656 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:42:25,724 In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: 2021-07-29T19:42:25,724 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:25,724 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:25,725 | 2021-07-29T19:42:25,729 In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: 2021-07-29T19:42:25,730 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:25,730 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:25,730 | 2021-07-29T19:42:25,730 In file included from /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2021-07-29T19:42:25,730 from MDAnalysis/lib/formats/src/trr_seek.c:31: 2021-07-29T19:42:25,730 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:25,730 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:25,731 | 2021-07-29T19:42:25,733 MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’: 2021-07-29T19:42:25,733 MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable] 2021-07-29T19:42:25,734 39 | int result, framebytes, totalframebytes; 2021-07-29T19:42:25,734 | ^~~~~~~~~~~~~~~ 2021-07-29T19:42:25,734 MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable] 2021-07-29T19:42:25,734 38 | float time, lambda; 2021-07-29T19:42:25,734 | ^~~~~~ 2021-07-29T19:42:25,735 MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable] 2021-07-29T19:42:25,735 38 | float time, lambda; 2021-07-29T19:42:25,735 | ^~~~ 2021-07-29T19:42:25,861 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:42:25,891 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:42:26,014 In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: 2021-07-29T19:42:26,014 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:26,015 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:26,015 | 2021-07-29T19:42:26,025 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’: 2021-07-29T19:42:26,026 MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-29T19:42:26,026 501 | while (size >= num && num_of_bits < 32) 2021-07-29T19:42:26,026 | ^~ 2021-07-29T19:42:26,027 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’: 2021-07-29T19:42:26,028 MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:42:26,028 547 | while (bytes[num_of_bytes] >= num) 2021-07-29T19:42:26,028 | ^~ 2021-07-29T19:42:26,029 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’: 2021-07-29T19:42:26,030 MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-29T19:42:26,030 656 | if (num_of_bits >= num_of_bytes * 8) 2021-07-29T19:42:26,030 | ^~ 2021-07-29T19:42:26,031 MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-29T19:42:26,031 658 | for (i = 0; i < num_of_bytes; i++) 2021-07-29T19:42:26,031 | ^ 2021-07-29T19:42:26,032 MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-29T19:42:26,032 666 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-29T19:42:26,032 | ^ 2021-07-29T19:42:26,033 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’: 2021-07-29T19:42:26,033 MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:42:26,033 706 | if (lastbits < num_of_bits) 2021-07-29T19:42:26,033 | ^ 2021-07-29T19:42:26,035 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-29T19:42:26,036 MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:42:26,036 816 | if(size3>xfp->buf1size) 2021-07-29T19:42:26,036 | ^ 2021-07-29T19:42:26,038 MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:42:26,038 868 | maxidx = (LASTIDXxfp->buf1size) 2021-07-29T19:42:26,042 | ^ 2021-07-29T19:42:26,046 MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-29T19:42:26,047 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-29T19:42:26,047 | ^ 2021-07-29T19:42:26,047 MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:42:26,047 1141 | maxidx = (LASTIDXxfp->buf1size) 2021-07-29T19:42:26,054 | ^ 2021-07-29T19:42:26,056 MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:42:26,056 1368 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-29T19:42:26,063 | ^ 2021-07-29T19:42:26,070 MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-29T19:42:26,070 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-29T19:42:26,070 | ^ 2021-07-29T19:42:26,071 MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-29T19:42:26,071 1624 | maxidx = (LASTIDX maxsize) 2021-07-29T19:42:27,741 | ^ 2021-07-29T19:42:27,742 MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here 2021-07-29T19:42:27,742 2335 | unsigned int size; 2021-07-29T19:42:27,742 | ^~~~ 2021-07-29T19:42:28,175 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2021-07-29T19:42:28,176 MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-29T19:42:28,176 1157 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2021-07-29T19:42:28,176 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-29T19:42:28,176 MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-29T19:42:28,176 1156 | abs(thiscoord[1] - prevcoord[1]) < larger && 2021-07-29T19:42:28,176 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-29T19:42:28,177 MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-29T19:42:28,177 1155 | abs(thiscoord[0] - prevcoord[0]) < larger && 2021-07-29T19:42:28,177 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-29T19:42:28,931 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2021-07-29T19:42:28,932 MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-29T19:42:28,932 1639 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2021-07-29T19:42:28,932 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-29T19:42:28,933 MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-29T19:42:28,933 1638 | abs(thiscoord[1] - prevcoord[1]) < larger && 2021-07-29T19:42:28,933 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-29T19:42:28,933 MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-29T19:42:28,934 1637 | abs(thiscoord[0] - prevcoord[0]) < larger && 2021-07-29T19:42:28,934 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2021-07-29T19:42:29,970 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/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:42:29,999 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:42:30,071 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: 2021-07-29T19:42:30,071 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:30,071 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:30,071 | 2021-07-29T19:42:30,076 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2021-07-29T19:42:30,076 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:30,076 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:30,076 | 2021-07-29T19:42:30,076 In file included from /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2021-07-29T19:42:30,077 from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2021-07-29T19:42:30,077 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:30,077 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:30,077 | 2021-07-29T19:42:30,078 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’: 2021-07-29T19:42:30,078 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] 2021-07-29T19:42:30,079 78 | if (slen != strlen(version) + 1) 2021-07-29T19:42:30,079 | ^~ 2021-07-29T19:42:30,079 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] 2021-07-29T19:42:30,079 86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) 2021-07-29T19:42:30,079 | ^~ 2021-07-29T19:42:30,095 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’: 2021-07-29T19:42:30,095 MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized] 2021-07-29T19:42:30,096 408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); 2021-07-29T19:42:30,096 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:42:31,186 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/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:42:31,214 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:42:31,244 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: 2021-07-29T19:42:31,245 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:31,245 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:31,245 | 2021-07-29T19:42:31,257 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2021-07-29T19:42:31,258 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:31,258 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:31,258 | 2021-07-29T19:42:31,259 In file included from /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2021-07-29T19:42:31,259 from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2021-07-29T19:42:31,259 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:31,259 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:31,259 | 2021-07-29T19:42:31,395 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/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:42:31,427 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:42:31,457 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: 2021-07-29T19:42:31,457 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:31,458 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:31,458 | 2021-07-29T19:42:31,469 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2021-07-29T19:42:31,470 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:31,470 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:31,470 | 2021-07-29T19:42:31,471 In file included from /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2021-07-29T19:42:31,471 from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2021-07-29T19:42:31,471 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2021-07-29T19:42:31,471 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2021-07-29T19:42:31,471 | 2021-07-29T19:42:31,644 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 2021-07-29T19:42:31,906 building 'MDAnalysis.lib.formats.cython_util' extension 2021-07-29T19:42:31,906 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/usr/local/lib/python3.9/dist-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 2021-07-29T19:42:31,940 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:42:32,290 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:42:32,290 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:42:32,290 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:42:32,290 from MDAnalysis/lib/formats/cython_util.c:649: 2021-07-29T19:42:32,291 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:42:32,291 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:42:32,291 | ^~~~~~~ 2021-07-29T19:42:49,055 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 2021-07-29T19:42:49,232 building 'MDAnalysis.analysis.encore.cutils' extension 2021-07-29T19:42:49,233 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-29T19:42:49,233 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore 2021-07-29T19:42:49,234 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/usr/local/lib/python3.9/dist-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 -funroll-loops -fsigned-zeros -O3 2021-07-29T19:42:49,267 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:42:49,615 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:42:49,615 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:42:49,615 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:42:49,615 from MDAnalysis/analysis/encore/cutils.c:649: 2021-07-29T19:42:49,615 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:42:49,616 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:42:49,616 | ^~~~~~~ 2021-07-29T19:42:51,735 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 2021-07-29T19:42:51,854 building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension 2021-07-29T19:42:51,855 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering 2021-07-29T19:42:51,856 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/src 2021-07-29T19:42:51,857 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 -funroll-loops -fsigned-zeros -O3 2021-07-29T19:42:51,887 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:42:52,242 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:42:52,243 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:42:52,243 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:42:52,243 from MDAnalysis/analysis/encore/clustering/affinityprop.c:655: 2021-07-29T19:42:52,243 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:42:52,243 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:42:52,244 | ^~~~~~~ 2021-07-29T19:43:02,442 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 -funroll-loops -fsigned-zeros -O3 2021-07-29T19:43:02,468 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:43:03,513 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 2021-07-29T19:43:03,664 building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension 2021-07-29T19:43:03,665 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-29T19:43:03,665 creating build/temp.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/src 2021-07-29T19:43:03,666 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 -funroll-loops -fsigned-zeros -O3 2021-07-29T19:43:03,697 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:43:04,646 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 -funroll-loops -fsigned-zeros -O3 2021-07-29T19:43:04,673 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:43:05,037 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:43:05,038 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:43:05,038 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:43:05,038 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:655: 2021-07-29T19:43:05,038 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:43:05,038 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:43:05,038 | ^~~~~~~ 2021-07-29T19:43:08,969 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 2021-07-29T19:43:09,103 building 'MDAnalysis.lib._cutil' extension 2021-07-29T19:43:09,103 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/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 2021-07-29T19:43:09,151 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:43:09,464 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:43:09,464 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:43:09,464 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:43:09,465 from MDAnalysis/lib/_cutil.cpp:669: 2021-07-29T19:43:09,465 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:43:09,465 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:43:09,465 | ^~~~~~~ 2021-07-29T19:43:12,404 In file included from MDAnalysis/lib/_cutil.cpp:697: 2021-07-29T19:43:12,404 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:854:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,405 854 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,405 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,405 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:818:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,405 818 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,405 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,406 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:790:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,406 790 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,406 | ^~~~~~~~~~~~~~ 2021-07-29T19:43:12,406 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:713:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,406 713 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,406 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,407 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:670:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,407 670 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,407 | ^~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,407 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:639:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,407 639 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,407 | ^~~~~~~~~~~ 2021-07-29T19:43:12,408 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:614:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,408 614 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,408 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,408 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:589:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,408 589 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,408 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,409 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:570:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,409 570 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2021-07-29T19:43:12,409 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,409 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:515:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,409 515 | static void _calc_self_distance_array_triclinic(coordinate* ref, int numref, 2021-07-29T19:43:12,409 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,409 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:482:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,409 482 | static void _calc_self_distance_array_ortho(coordinate* ref, int numref, 2021-07-29T19:43:12,410 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,410 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:455:13: warning: ‘void _calc_self_distance_array(float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,410 455 | static void _calc_self_distance_array(coordinate* ref, int numref, 2021-07-29T19:43:12,410 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,410 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:428:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,410 428 | static void _calc_distance_array_triclinic(coordinate* ref, int numref, 2021-07-29T19:43:12,410 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,411 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:401:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,411 401 | static void _calc_distance_array_ortho(coordinate* ref, int numref, coordinate* conf, 2021-07-29T19:43:12,411 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,411 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:380:13: warning: ‘void _calc_distance_array(float (*)[3], int, float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,411 380 | static void _calc_distance_array(coordinate* ref, int numref, coordinate* conf, 2021-07-29T19:43:12,411 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:43:12,411 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:111:13: warning: ‘void _ortho_pbc(float (*)[3], int, float*)’ defined but not used [-Wunused-function] 2021-07-29T19:43:12,411 111 | static void _ortho_pbc(coordinate* coords, int numcoords, float* box) 2021-07-29T19:43:12,412 | ^~~~~~~~~~ 2021-07-29T19:43:38,877 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 2021-07-29T19:43:39,261 building 'MDAnalysis.lib._augment' extension 2021-07-29T19:43:39,261 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/usr/local/lib/python3.9/dist-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 2021-07-29T19:43:39,292 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:43:39,542 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-29T19:43:39,542 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-29T19:43:39,542 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-29T19:43:39,542 from MDAnalysis/lib/_augment.cpp:664: 2021-07-29T19:43:39,543 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-29T19:43:39,543 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-29T19:43:39,543 | ^~~~~~~ 2021-07-29T19:44:05,258 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 2021-07-29T19:44:05,601 building 'MDAnalysis.lib.nsgrid' extension 2021-07-29T19:44:05,602 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/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 2021-07-29T19:44:05,638 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2021-07-29T19:44:08,075 In file included from MDAnalysis/lib/nsgrid.cpp:665: 2021-07-29T19:44:08,075 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:854:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,076 854 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,076 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,076 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:818:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,076 818 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,076 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,077 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:790:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,077 790 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,077 | ^~~~~~~~~~~~~~ 2021-07-29T19:44:08,077 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:713:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,077 713 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,078 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,078 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:670:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,078 670 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,078 | ^~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,078 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:639:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,078 639 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,079 | ^~~~~~~~~~~ 2021-07-29T19:44:08,079 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:614:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,079 614 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,079 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,079 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:589:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,079 589 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,079 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,079 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:570:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,080 570 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2021-07-29T19:44:08,080 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,080 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:515:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,080 515 | static void _calc_self_distance_array_triclinic(coordinate* ref, int numref, 2021-07-29T19:44:08,080 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,080 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:482:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,080 482 | static void _calc_self_distance_array_ortho(coordinate* ref, int numref, 2021-07-29T19:44:08,080 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,081 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:455:13: warning: ‘void _calc_self_distance_array(float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,081 455 | static void _calc_self_distance_array(coordinate* ref, int numref, 2021-07-29T19:44:08,081 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,081 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:428:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,081 428 | static void _calc_distance_array_triclinic(coordinate* ref, int numref, 2021-07-29T19:44:08,081 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,081 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:401:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], int, float (*)[3], int, float*, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,082 401 | static void _calc_distance_array_ortho(coordinate* ref, int numref, coordinate* conf, 2021-07-29T19:44:08,082 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:08,082 /tmp/pip-wheel-9jkjktma/mdanalysis_65d4a13b90e3442696d18dee5df5e7d7/MDAnalysis/lib/include/calc_distances.h:380:13: warning: ‘void _calc_distance_array(float (*)[3], int, float (*)[3], int, double*)’ defined but not used [-Wunused-function] 2021-07-29T19:44:08,082 380 | static void _calc_distance_array(coordinate* ref, int numref, coordinate* conf, 2021-07-29T19:44:08,082 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:30,682 In file included from /usr/include/c++/10/vector:72, 2021-07-29T19:44:30,682 from MDAnalysis/lib/nsgrid.cpp:663: 2021-07-29T19:44:30,683 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2021-07-29T19:44:30,683 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T19:44:30,683 426 | vector<_Tp, _Alloc>:: 2021-07-29T19:44:30,683 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:30,719 In file included from /usr/include/c++/10/vector:67, 2021-07-29T19:44:30,719 from MDAnalysis/lib/nsgrid.cpp:663: 2021-07-29T19:44:30,719 /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*, int, int, double)’: 2021-07-29T19:44:30,719 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T19:44:30,720 1198 | _M_realloc_insert(end(), __x); 2021-07-29T19:44:30,720 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-29T19:44:30,756 In file included from /usr/include/c++/10/vector:72, 2021-07-29T19:44:30,757 from MDAnalysis/lib/nsgrid.cpp:663: 2021-07-29T19:44:30,757 /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 = {double}; _Tp = double; _Alloc = std::allocator]’: 2021-07-29T19:44:30,757 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-29T19:44:30,757 426 | vector<_Tp, _Alloc>:: 2021-07-29T19:44:30,757 | ^~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:31,010 /usr/include/c++/10/bits/vector.tcc: In function ‘PyObject* __pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults__set_state(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, PyObject*)’: 2021-07-29T19:44:31,010 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-29T19:44:31,010 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-29T19:44:31,010 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-29T19:44:34,407 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 2021-07-29T19:44:34,797 installing to build/bdist.linux-armv7l/wheel 2021-07-29T19:44:34,797 running install 2021-07-29T19:44:34,798 running install_lib 2021-07-29T19:44:34,802 creating build/bdist.linux-armv7l 2021-07-29T19:44:34,802 creating build/bdist.linux-armv7l/wheel 2021-07-29T19:44:34,804 creating build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-29T19:44:34,805 copying build/lib.linux-armv7l-3.9/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-29T19:44:34,807 copying build/lib.linux-armv7l-3.9/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-29T19:44:34,810 creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-29T19:44:34,810 copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-29T19:44:34,812 copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-29T19:44:34,815 copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-29T19:44:34,817 copying build/lib.linux-armv7l-3.9/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2021-07-29T19:44:34,821 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,822 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,824 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,826 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,828 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,830 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,833 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,835 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,837 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,839 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,840 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,843 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,845 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,848 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,850 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,853 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,856 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,858 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,860 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,863 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,865 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-29T19:44:34,866 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-29T19:44:34,869 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-29T19:44:34,871 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-29T19:44:34,874 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-29T19:44:34,876 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,879 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,881 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,884 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,886 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,889 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,891 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,893 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,895 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-29T19:44:34,899 creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-29T19:44:34,900 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-29T19:44:34,902 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-29T19:44:34,904 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-29T19:44:34,905 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-29T19:44:34,908 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-29T19:44:34,910 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-29T19:44:34,912 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-29T19:44:34,915 creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,916 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,918 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,920 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/wrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,923 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,925 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,927 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,930 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,932 copying build/lib.linux-armv7l-3.9/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2021-07-29T19:44:34,935 creating build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,936 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/accessors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,938 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,941 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,945 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,947 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,951 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,956 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,959 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,963 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-29T19:44:34,971 creating build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2021-07-29T19:44:34,971 copying build/lib.linux-armv7l-3.9/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2021-07-29T19:44:34,974 copying build/lib.linux-armv7l-3.9/MDAnalysis/converters/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2021-07-29T19:44:34,976 copying build/lib.linux-armv7l-3.9/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2021-07-29T19:44:34,979 copying build/lib.linux-armv7l-3.9/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2021-07-29T19:44:34,981 copying build/lib.linux-armv7l-3.9/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2021-07-29T19:44:34,984 copying build/lib.linux-armv7l-3.9/MDAnalysis/converters/RDKit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2021-07-29T19:44:34,987 copying build/lib.linux-armv7l-3.9/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2021-07-29T19:44:34,991 creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-29T19:44:34,991 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-29T19:44:34,995 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-29T19:44:34,997 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-29T19:44:34,999 copying build/lib.linux-armv7l-3.9/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-29T19:44:35,001 copying build/lib.linux-armv7l-3.9/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-29T19:44:35,005 creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-29T19:44:35,006 copying build/lib.linux-armv7l-3.9/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-29T19:44:35,008 copying build/lib.linux-armv7l-3.9/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-29T19:44:35,011 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,012 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,015 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,017 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,020 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,023 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,026 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,030 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,032 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,035 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,038 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,040 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,043 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,046 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,049 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,051 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,055 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,058 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,061 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,065 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,067 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,070 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,072 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,075 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,078 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,081 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,084 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,086 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,092 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,095 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,098 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,101 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,103 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-29T19:44:35,105 copying build/lib.linux-armv7l-3.9/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-29T19:44:35,108 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,109 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,112 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,143 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,146 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,158 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,162 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,173 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 2021-07-29T19:44:35,183 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,189 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2021-07-29T19:44:35,190 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 2021-07-29T19:44:35,217 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 2021-07-29T19:44:35,263 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2021-07-29T19:44:35,265 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 2021-07-29T19:44:35,311 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,363 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,365 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,368 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,371 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,374 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,414 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/correlations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,416 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,419 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-29T19:44:35,465 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,466 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,469 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,472 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,474 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,476 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,479 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,484 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,488 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-29T19:44:35,489 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-29T19:44:35,492 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-29T19:44:35,495 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:44:35,496 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:44:35,499 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:44:35,501 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:44:35,505 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2021-07-29T19:44:35,510 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,513 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,515 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,519 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,522 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,528 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-29T19:44:35,529 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-29T19:44:35,533 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-29T19:44:35,535 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-29T19:44:35,538 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-29T19:44:35,541 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-29T19:44:35,544 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 2021-07-29T19:44:35,551 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-29T19:44:35,552 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-29T19:44:35,554 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-29T19:44:35,557 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-29T19:44:35,560 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 2021-07-29T19:44:35,577 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2021-07-29T19:44:35,580 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-29T19:44:35,581 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 2021-07-29T19:44:35,584 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-29T19:44:35,587 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2021-07-29T19:44:35,589 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 2021-07-29T19:44:35,599 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2021-07-29T19:44:35,602 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,605 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,609 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-29T19:44:35,610 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-29T19:44:35,613 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-29T19:44:35,615 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-29T19:44:35,617 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2021-07-29T19:44:35,622 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,624 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,627 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2021-07-29T19:44:35,628 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2021-07-29T19:44:35,631 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2021-07-29T19:44:35,633 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2021-07-29T19:44:35,636 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2021-07-29T19:44:35,639 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/msd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,642 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/bat.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,646 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2021-07-29T19:44:35,647 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2021-07-29T19:44:35,649 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2021-07-29T19:44:35,652 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,655 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,658 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-29T19:44:35,661 copying build/lib.linux-armv7l-3.9/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-29T19:44:35,663 running install_egg_info 2021-07-29T19:44:35,689 running egg_info 2021-07-29T19:44:35,690 writing MDAnalysis.egg-info/PKG-INFO 2021-07-29T19:44:35,692 writing dependency_links to MDAnalysis.egg-info/dependency_links.txt 2021-07-29T19:44:35,693 writing requirements to MDAnalysis.egg-info/requires.txt 2021-07-29T19:44:35,694 writing top-level names to MDAnalysis.egg-info/top_level.txt 2021-07-29T19:44:35,749 reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2021-07-29T19:44:35,803 reading manifest template 'MANIFEST.in' 2021-07-29T19:44:36,080 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2021-07-29T19:44:36,083 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-29T19:44:36,085 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2021-07-29T19:44:36,088 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2021-07-29T19:44:36,091 warning: no previously-included files matching '*~' found anywhere in distribution 2021-07-29T19:44:36,094 warning: no previously-included files matching '.git' found anywhere in distribution 2021-07-29T19:44:36,094 adding license file 'LICENSE' 2021-07-29T19:44:36,094 adding license file 'AUTHORS' 2021-07-29T19:44:36,118 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2021-07-29T19:44:36,120 Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-2.0.0b0-py3.9.egg-info 2021-07-29T19:44:36,133 running install_scripts 2021-07-29T19:44:36,197 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-29T19:44:36,198 adding license file "AUTHORS" (matched pattern "AUTHORS*") 2021-07-29T19:44:36,204 creating build/bdist.linux-armv7l/wheel/MDAnalysis-2.0.0b0.dist-info/WHEEL 2021-07-29T19:44:36,207 creating '/tmp/pip-wheel-a4qrqsvq/MDAnalysis-2.0.0b0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-29T19:44:36,210 adding 'MDAnalysis/__init__.py' 2021-07-29T19:44:36,212 adding 'MDAnalysis/authors.py' 2021-07-29T19:44:36,214 adding 'MDAnalysis/due.py' 2021-07-29T19:44:36,215 adding 'MDAnalysis/exceptions.py' 2021-07-29T19:44:36,218 adding 'MDAnalysis/units.py' 2021-07-29T19:44:36,219 adding 'MDAnalysis/version.py' 2021-07-29T19:44:36,221 adding 'MDAnalysis/analysis/__init__.py' 2021-07-29T19:44:36,230 adding 'MDAnalysis/analysis/align.py' 2021-07-29T19:44:36,234 adding 'MDAnalysis/analysis/base.py' 2021-07-29T19:44:36,238 adding 'MDAnalysis/analysis/bat.py' 2021-07-29T19:44:36,241 adding 'MDAnalysis/analysis/contacts.py' 2021-07-29T19:44:36,247 adding 'MDAnalysis/analysis/density.py' 2021-07-29T19:44:36,250 adding 'MDAnalysis/analysis/diffusionmap.py' 2021-07-29T19:44:36,254 adding 'MDAnalysis/analysis/dihedrals.py' 2021-07-29T19:44:36,256 adding 'MDAnalysis/analysis/distances.py' 2021-07-29T19:44:36,259 adding 'MDAnalysis/analysis/gnm.py' 2021-07-29T19:44:36,262 adding 'MDAnalysis/analysis/helix_analysis.py' 2021-07-29T19:44:36,264 adding 'MDAnalysis/analysis/leaflet.py' 2021-07-29T19:44:36,267 adding 'MDAnalysis/analysis/lineardensity.py' 2021-07-29T19:44:36,269 adding 'MDAnalysis/analysis/msd.py' 2021-07-29T19:44:36,272 adding 'MDAnalysis/analysis/nuclinfo.py' 2021-07-29T19:44:36,275 adding 'MDAnalysis/analysis/pca.py' 2021-07-29T19:44:36,277 adding 'MDAnalysis/analysis/polymer.py' 2021-07-29T19:44:36,288 adding 'MDAnalysis/analysis/psa.py' 2021-07-29T19:44:36,292 adding 'MDAnalysis/analysis/rdf.py' 2021-07-29T19:44:36,297 adding 'MDAnalysis/analysis/rms.py' 2021-07-29T19:44:36,302 adding 'MDAnalysis/analysis/waterdynamics.py' 2021-07-29T19:44:36,304 adding 'MDAnalysis/analysis/data/__init__.py' 2021-07-29T19:44:36,306 adding 'MDAnalysis/analysis/data/filenames.py' 2021-07-29T19:44:36,310 adding 'MDAnalysis/analysis/data/janin_ref_data.npy' 2021-07-29T19:44:36,315 adding 'MDAnalysis/analysis/data/rama_ref_data.npy' 2021-07-29T19:44:36,318 adding 'MDAnalysis/analysis/encore/__init__.py' 2021-07-29T19:44:36,320 adding 'MDAnalysis/analysis/encore/bootstrap.py' 2021-07-29T19:44:36,322 adding 'MDAnalysis/analysis/encore/confdistmatrix.py' 2021-07-29T19:44:36,324 adding 'MDAnalysis/analysis/encore/covariance.py' 2021-07-29T19:44:36,354 adding 'MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:36,362 adding 'MDAnalysis/analysis/encore/similarity.py' 2021-07-29T19:44:36,365 adding 'MDAnalysis/analysis/encore/utils.py' 2021-07-29T19:44:36,367 adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' 2021-07-29T19:44:36,369 adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' 2021-07-29T19:44:36,371 adding 'MDAnalysis/analysis/encore/clustering/__init__.py' 2021-07-29T19:44:36,473 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:36,478 adding 'MDAnalysis/analysis/encore/clustering/cluster.py' 2021-07-29T19:44:36,480 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' 2021-07-29T19:44:36,482 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' 2021-07-29T19:44:36,483 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' 2021-07-29T19:44:36,544 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:36,547 adding 'MDAnalysis/analysis/hbonds/__init__.py' 2021-07-29T19:44:36,549 adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' 2021-07-29T19:44:36,550 adding 'MDAnalysis/analysis/hole2/__init__.py' 2021-07-29T19:44:36,556 adding 'MDAnalysis/analysis/hole2/hole.py' 2021-07-29T19:44:36,558 adding 'MDAnalysis/analysis/hole2/templates.py' 2021-07-29T19:44:36,561 adding 'MDAnalysis/analysis/hole2/utils.py' 2021-07-29T19:44:36,563 adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' 2021-07-29T19:44:36,567 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' 2021-07-29T19:44:36,570 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' 2021-07-29T19:44:36,580 adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' 2021-07-29T19:44:36,582 adding 'MDAnalysis/analysis/legacy/__init__.py' 2021-07-29T19:44:36,587 adding 'MDAnalysis/analysis/legacy/x3dna.py' 2021-07-29T19:44:36,589 adding 'MDAnalysis/auxiliary/XVG.py' 2021-07-29T19:44:36,592 adding 'MDAnalysis/auxiliary/__init__.py' 2021-07-29T19:44:36,597 adding 'MDAnalysis/auxiliary/base.py' 2021-07-29T19:44:36,598 adding 'MDAnalysis/auxiliary/core.py' 2021-07-29T19:44:36,600 adding 'MDAnalysis/converters/OpenMM.py' 2021-07-29T19:44:36,602 adding 'MDAnalysis/converters/OpenMMParser.py' 2021-07-29T19:44:36,604 adding 'MDAnalysis/converters/ParmEd.py' 2021-07-29T19:44:36,606 adding 'MDAnalysis/converters/ParmEdParser.py' 2021-07-29T19:44:36,610 adding 'MDAnalysis/converters/RDKit.py' 2021-07-29T19:44:36,613 adding 'MDAnalysis/converters/RDKitParser.py' 2021-07-29T19:44:36,614 adding 'MDAnalysis/converters/__init__.py' 2021-07-29T19:44:36,616 adding 'MDAnalysis/coordinates/CRD.py' 2021-07-29T19:44:36,619 adding 'MDAnalysis/coordinates/DCD.py' 2021-07-29T19:44:36,621 adding 'MDAnalysis/coordinates/DLPoly.py' 2021-07-29T19:44:36,622 adding 'MDAnalysis/coordinates/DMS.py' 2021-07-29T19:44:36,624 adding 'MDAnalysis/coordinates/FHIAIMS.py' 2021-07-29T19:44:36,626 adding 'MDAnalysis/coordinates/GMS.py' 2021-07-29T19:44:36,629 adding 'MDAnalysis/coordinates/GRO.py' 2021-07-29T19:44:36,631 adding 'MDAnalysis/coordinates/GSD.py' 2021-07-29T19:44:36,634 adding 'MDAnalysis/coordinates/H5MD.py' 2021-07-29T19:44:36,636 adding 'MDAnalysis/coordinates/INPCRD.py' 2021-07-29T19:44:36,639 adding 'MDAnalysis/coordinates/LAMMPS.py' 2021-07-29T19:44:36,641 adding 'MDAnalysis/coordinates/MMTF.py' 2021-07-29T19:44:36,643 adding 'MDAnalysis/coordinates/MOL2.py' 2021-07-29T19:44:36,644 adding 'MDAnalysis/coordinates/NAMDBIN.py' 2021-07-29T19:44:36,651 adding 'MDAnalysis/coordinates/PDB.py' 2021-07-29T19:44:36,654 adding 'MDAnalysis/coordinates/PDBQT.py' 2021-07-29T19:44:36,656 adding 'MDAnalysis/coordinates/PQR.py' 2021-07-29T19:44:36,658 adding 'MDAnalysis/coordinates/ParmEd.py' 2021-07-29T19:44:36,664 adding 'MDAnalysis/coordinates/TRJ.py' 2021-07-29T19:44:36,666 adding 'MDAnalysis/coordinates/TRR.py' 2021-07-29T19:44:36,668 adding 'MDAnalysis/coordinates/TRZ.py' 2021-07-29T19:44:36,670 adding 'MDAnalysis/coordinates/TXYZ.py' 2021-07-29T19:44:36,672 adding 'MDAnalysis/coordinates/XDR.py' 2021-07-29T19:44:36,674 adding 'MDAnalysis/coordinates/XTC.py' 2021-07-29T19:44:36,678 adding 'MDAnalysis/coordinates/XYZ.py' 2021-07-29T19:44:36,683 adding 'MDAnalysis/coordinates/__init__.py' 2021-07-29T19:44:36,693 adding 'MDAnalysis/coordinates/base.py' 2021-07-29T19:44:36,697 adding 'MDAnalysis/coordinates/chain.py' 2021-07-29T19:44:36,700 adding 'MDAnalysis/coordinates/chemfiles.py' 2021-07-29T19:44:36,702 adding 'MDAnalysis/coordinates/core.py' 2021-07-29T19:44:36,705 adding 'MDAnalysis/coordinates/memory.py' 2021-07-29T19:44:36,707 adding 'MDAnalysis/coordinates/null.py' 2021-07-29T19:44:36,708 adding 'MDAnalysis/core/__init__.py' 2021-07-29T19:44:36,710 adding 'MDAnalysis/core/_get_readers.py' 2021-07-29T19:44:36,712 adding 'MDAnalysis/core/accessors.py' 2021-07-29T19:44:36,733 adding 'MDAnalysis/core/groups.py' 2021-07-29T19:44:36,741 adding 'MDAnalysis/core/selection.py' 2021-07-29T19:44:36,744 adding 'MDAnalysis/core/topology.py' 2021-07-29T19:44:36,753 adding 'MDAnalysis/core/topologyattrs.py' 2021-07-29T19:44:36,758 adding 'MDAnalysis/core/topologyobjects.py' 2021-07-29T19:44:36,765 adding 'MDAnalysis/core/universe.py' 2021-07-29T19:44:36,768 adding 'MDAnalysis/lib/NeighborSearch.py' 2021-07-29T19:44:36,769 adding 'MDAnalysis/lib/__init__.py' 2021-07-29T19:44:37,033 adding 'MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:37,390 adding 'MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:37,459 adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:37,707 adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:37,770 adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:37,774 adding 'MDAnalysis/lib/correlations.py' 2021-07-29T19:44:37,779 adding 'MDAnalysis/lib/distances.py' 2021-07-29T19:44:37,782 adding 'MDAnalysis/lib/log.py' 2021-07-29T19:44:37,784 adding 'MDAnalysis/lib/mdamath.py' 2021-07-29T19:44:38,117 adding 'MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:38,133 adding 'MDAnalysis/lib/picklable_file_io.py' 2021-07-29T19:44:38,135 adding 'MDAnalysis/lib/pkdtree.py' 2021-07-29T19:44:38,205 adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:38,215 adding 'MDAnalysis/lib/transformations.py' 2021-07-29T19:44:38,229 adding 'MDAnalysis/lib/util.py' 2021-07-29T19:44:38,231 adding 'MDAnalysis/lib/formats/__init__.py' 2021-07-29T19:44:38,440 adding 'MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:38,842 adding 'MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:39,263 adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so' 2021-07-29T19:44:39,281 adding 'MDAnalysis/selections/__init__.py' 2021-07-29T19:44:39,283 adding 'MDAnalysis/selections/base.py' 2021-07-29T19:44:39,284 adding 'MDAnalysis/selections/charmm.py' 2021-07-29T19:44:39,286 adding 'MDAnalysis/selections/gromacs.py' 2021-07-29T19:44:39,287 adding 'MDAnalysis/selections/jmol.py' 2021-07-29T19:44:39,288 adding 'MDAnalysis/selections/pymol.py' 2021-07-29T19:44:39,290 adding 'MDAnalysis/selections/vmd.py' 2021-07-29T19:44:39,292 adding 'MDAnalysis/tests/__init__.py' 2021-07-29T19:44:39,293 adding 'MDAnalysis/tests/datafiles.py' 2021-07-29T19:44:39,295 adding 'MDAnalysis/topology/CRDParser.py' 2021-07-29T19:44:39,297 adding 'MDAnalysis/topology/DLPolyParser.py' 2021-07-29T19:44:39,299 adding 'MDAnalysis/topology/DMSParser.py' 2021-07-29T19:44:39,300 adding 'MDAnalysis/topology/ExtendedPDBParser.py' 2021-07-29T19:44:39,302 adding 'MDAnalysis/topology/FHIAIMSParser.py' 2021-07-29T19:44:39,304 adding 'MDAnalysis/topology/GMSParser.py' 2021-07-29T19:44:39,305 adding 'MDAnalysis/topology/GROParser.py' 2021-07-29T19:44:39,307 adding 'MDAnalysis/topology/GSDParser.py' 2021-07-29T19:44:39,309 adding 'MDAnalysis/topology/HoomdXMLParser.py' 2021-07-29T19:44:39,313 adding 'MDAnalysis/topology/ITPParser.py' 2021-07-29T19:44:39,316 adding 'MDAnalysis/topology/LAMMPSParser.py' 2021-07-29T19:44:39,319 adding 'MDAnalysis/topology/MMTFParser.py' 2021-07-29T19:44:39,321 adding 'MDAnalysis/topology/MOL2Parser.py' 2021-07-29T19:44:39,323 adding 'MDAnalysis/topology/MinimalParser.py' 2021-07-29T19:44:39,325 adding 'MDAnalysis/topology/PDBParser.py' 2021-07-29T19:44:39,327 adding 'MDAnalysis/topology/PDBQTParser.py' 2021-07-29T19:44:39,329 adding 'MDAnalysis/topology/PQRParser.py' 2021-07-29T19:44:39,331 adding 'MDAnalysis/topology/PSFParser.py' 2021-07-29T19:44:39,333 adding 'MDAnalysis/topology/ParmEdParser.py' 2021-07-29T19:44:39,336 adding 'MDAnalysis/topology/TOPParser.py' 2021-07-29T19:44:39,339 adding 'MDAnalysis/topology/TPRParser.py' 2021-07-29T19:44:39,340 adding 'MDAnalysis/topology/TXYZParser.py' 2021-07-29T19:44:39,342 adding 'MDAnalysis/topology/XYZParser.py' 2021-07-29T19:44:39,345 adding 'MDAnalysis/topology/__init__.py' 2021-07-29T19:44:39,347 adding 'MDAnalysis/topology/base.py' 2021-07-29T19:44:39,348 adding 'MDAnalysis/topology/core.py' 2021-07-29T19:44:39,351 adding 'MDAnalysis/topology/guessers.py' 2021-07-29T19:44:39,354 adding 'MDAnalysis/topology/tables.py' 2021-07-29T19:44:39,356 adding 'MDAnalysis/topology/tpr/__init__.py' 2021-07-29T19:44:39,358 adding 'MDAnalysis/topology/tpr/obj.py' 2021-07-29T19:44:39,360 adding 'MDAnalysis/topology/tpr/setting.py' 2021-07-29T19:44:39,365 adding 'MDAnalysis/topology/tpr/utils.py' 2021-07-29T19:44:39,367 adding 'MDAnalysis/transformations/__init__.py' 2021-07-29T19:44:39,369 adding 'MDAnalysis/transformations/base.py' 2021-07-29T19:44:39,371 adding 'MDAnalysis/transformations/boxdimensions.py' 2021-07-29T19:44:39,373 adding 'MDAnalysis/transformations/fit.py' 2021-07-29T19:44:39,375 adding 'MDAnalysis/transformations/positionaveraging.py' 2021-07-29T19:44:39,377 adding 'MDAnalysis/transformations/rotate.py' 2021-07-29T19:44:39,379 adding 'MDAnalysis/transformations/translate.py' 2021-07-29T19:44:39,380 adding 'MDAnalysis/transformations/wrap.py' 2021-07-29T19:44:39,382 adding 'MDAnalysis/visualization/__init__.py' 2021-07-29T19:44:39,385 adding 'MDAnalysis/visualization/streamlines.py' 2021-07-29T19:44:39,389 adding 'MDAnalysis/visualization/streamlines_3D.py' 2021-07-29T19:44:39,392 adding 'MDAnalysis-2.0.0b0.dist-info/AUTHORS' 2021-07-29T19:44:39,396 adding 'MDAnalysis-2.0.0b0.dist-info/LICENSE' 2021-07-29T19:44:39,398 adding 'MDAnalysis-2.0.0b0.dist-info/METADATA' 2021-07-29T19:44:39,399 adding 'MDAnalysis-2.0.0b0.dist-info/WHEEL' 2021-07-29T19:44:39,400 adding 'MDAnalysis-2.0.0b0.dist-info/top_level.txt' 2021-07-29T19:44:39,403 adding 'MDAnalysis-2.0.0b0.dist-info/RECORD' 2021-07-29T19:44:39,486 removing build/bdist.linux-armv7l/wheel 2021-07-29T19:44:39,705 Building wheel for mdanalysis (setup.py): finished with status 'done' 2021-07-29T19:44:39,783 Created wheel for mdanalysis: filename=MDAnalysis-2.0.0b0-cp39-cp39-linux_armv7l.whl size=5655745 sha256=6faa74b3b1a64cdd53a1313f3ecf13a260e99df077e63a45b273edd2b5afc680 2021-07-29T19:44:39,784 Stored in directory: /tmp/pip-ephem-wheel-cache-p8_kbzny/wheels/5e/a7/28/1c392640be72c44d40adeefd5ea798b0e67d685eca30c253e9 2021-07-29T19:44:39,804 Successfully built mdanalysis 2021-07-29T19:44:40,016 Removed build tracker: '/tmp/pip-req-tracker-bq_o6689'