2021-07-10T11:34:46,697 Created temporary directory: /tmp/pip-ephem-wheel-cache-ykpl05dh 2021-07-10T11:34:46,701 Created temporary directory: /tmp/pip-req-tracker-s6dsc3z7 2021-07-10T11:34:46,701 Initialized build tracking at /tmp/pip-req-tracker-s6dsc3z7 2021-07-10T11:34:46,702 Created build tracker: /tmp/pip-req-tracker-s6dsc3z7 2021-07-10T11:34:46,702 Entered build tracker: /tmp/pip-req-tracker-s6dsc3z7 2021-07-10T11:34:46,703 Created temporary directory: /tmp/pip-wheel-cct7jbri 2021-07-10T11:34:46,734 1 location(s) to search for versions of mdanalysis: 2021-07-10T11:34:46,734 * https://pypi.org/simple/mdanalysis/ 2021-07-10T11:34:46,735 Fetching project page and analyzing links: https://pypi.org/simple/mdanalysis/ 2021-07-10T11:34:46,735 Getting page https://pypi.org/simple/mdanalysis/ 2021-07-10T11:34:46,737 Found index url https://pypi.org/simple 2021-07-10T11:34:46,932 Found link https://files.pythonhosted.org/packages/97/94/fd5a74e25fba58cfb514dc39ef4717baa392057503d6c38897f886b2c0c6/MDAnalysis-0.7.6.tar.gz#sha256=4225660533926ce808ae425f22edc643db296274ac3b95d9feae4eec0b38ff24 (from https://pypi.org/simple/mdanalysis/), version: 0.7.6 2021-07-10T11:34:46,932 Found link https://files.pythonhosted.org/packages/9d/32/36e44fd1b946331bd72c7cc8806dd2b37f597a49ac7ccfe2a64ad91e59f7/MDAnalysis-0.8.0rc2.tar.gz#sha256=5e14ea8593b80d93a75e4445965f79fb245a7b581ebc8389b9360b9145e88f32 (from https://pypi.org/simple/mdanalysis/), version: 0.8.0rc2 2021-07-10T11:34:46,933 Found link https://files.pythonhosted.org/packages/d9/c4/27ff9dcd35aeef52f41f01a6eff0328eda8a5fa6dfa8097daa9ff70dcdf8/MDAnalysis-0.8.0rc4.tar.gz#sha256=881af3c86c796995d3c48f803227ff9ae7c3f0b8f5b86e382ea0e24feda222c6 (from https://pypi.org/simple/mdanalysis/), version: 0.8.0rc4 2021-07-10T11:34:46,933 Found link 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https://files.pythonhosted.org/packages/9e/19/1d32ded1891605facf6faf6e0de4ff6bd33db3f7983d84cfc10074363990/MDAnalysis-1.0.1.tar.gz#sha256=dc2cf34391b5eb1733fca1ab14e0de2e381d2d595c95923403f42cb2e39c9dad (from https://pypi.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2021-07-10T11:34:46,942 Link requires a different Python (3.9.2 not in: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9'): https://files.pythonhosted.org/packages/0f/5a/3f34615abbe7c7758847636167d0caad7bb428c3950da64e7a3003b2c6fc/MDAnalysis-1.1.0.tar.gz#sha256=17cafb982e4380d62c6e2ba951c7717e9393b4c7b6200b6632763100ea2b0839 (from https://pypi.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2021-07-10T11:34:46,942 Link requires a different Python (3.9.2 not in: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9'): https://files.pythonhosted.org/packages/43/64/5fc4d327f242130f983b9a1ded4a406191385370dbc55a7be99f8ead126d/MDAnalysis-1.1.1.tar.gz#sha256=edfd5a8ac6cbaa8d02f505ac3e68d5a1866644a2d392a8f20e279c43e0886253 (from https://pypi.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2021-07-10T11:34:46,943 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 2021-07-10T11:34:46,943 Skipping link: not a file: https://pypi.org/simple/mdanalysis/ 2021-07-10T11:34:46,964 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates 2021-07-10T11:34:46,984 Collecting mdanalysis==0.13.0 2021-07-10T11:34:46,985 Created temporary directory: /tmp/pip-unpack-d5f26jw8 2021-07-10T11:34:48,034 Downloading MDAnalysis-0.13.0.tar.gz (3.1 MB) 2021-07-10T11:34:49,700 Added mdanalysis==0.13.0 from https://files.pythonhosted.org/packages/78/33/704a708797267b35bfe27cc40e83eedabad62c7bb143babbc728ee285082/MDAnalysis-0.13.0.tar.gz#sha256=bdf5a15842bd4e4635fcb60297978252c55c5828c9b7003d810c9e19a4fffbe6 to build tracker '/tmp/pip-req-tracker-s6dsc3z7' 2021-07-10T11:34:49,702 Running setup.py (path:/tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/setup.py) egg_info for package mdanalysis 2021-07-10T11:34:49,703 Created temporary directory: /tmp/pip-pip-egg-info-r7n6j1sg 2021-07-10T11:34:49,703 Running command python setup.py egg_info 2021-07-10T11:34:50,663 /tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/setup.py:103: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. 2021-07-10T11:34:50,664 self.config = configparser.SafeConfigParser() 2021-07-10T11:34:51,919 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/MDAnalysis/coordinates/dcdtimeseries.pyx 2021-07-10T11:34:51,919 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-10T11:34:53,240 warning: MDAnalysis/coordinates/dcdtimeseries.pyx:66:15: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2021-07-10T11:34:53,240 warning: MDAnalysis/coordinates/dcdtimeseries.pyx:66:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2021-07-10T11:34:53,240 warning: MDAnalysis/coordinates/dcdtimeseries.pyx:66:31: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2021-07-10T11:34:53,245 warning: MDAnalysis/coordinates/dcdtimeseries.pyx:140:15: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2021-07-10T11:34:53,245 warning: MDAnalysis/coordinates/dcdtimeseries.pyx:140:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2021-07-10T11:34:53,245 warning: MDAnalysis/coordinates/dcdtimeseries.pyx:140:31: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2021-07-10T11:34:53,588 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/MDAnalysis/lib/c_distances.pyx 2021-07-10T11:34:53,588 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-10T11:35:00,318 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/MDAnalysis/lib/c_distances_openmp.pyx 2021-07-10T11:35:00,319 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-10T11:35:01,965 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/MDAnalysis/lib/qcprot.pyx 2021-07-10T11:35:01,965 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-10T11:35:04,044 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-10T11:35:04,044 Compiling MDAnalysis/coordinates/dcdtimeseries.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-10T11:35:04,044 Compiling MDAnalysis/lib/c_distances.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-10T11:35:04,044 Compiling MDAnalysis/lib/c_distances_openmp.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-10T11:35:04,044 Compiling MDAnalysis/lib/qcprot.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd. 2021-07-10T11:35:04,044 [1/4] Cythonizing MDAnalysis/coordinates/dcdtimeseries.pyx 2021-07-10T11:35:04,044 [2/4] Cythonizing MDAnalysis/lib/c_distances.pyx 2021-07-10T11:35:04,045 [3/4] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx 2021-07-10T11:35:04,045 [4/4] Cythonizing MDAnalysis/lib/qcprot.pyx 2021-07-10T11:35:04,273 running egg_info 2021-07-10T11:35:04,276 creating /tmp/pip-pip-egg-info-r7n6j1sg/MDAnalysis.egg-info 2021-07-10T11:35:04,277 writing /tmp/pip-pip-egg-info-r7n6j1sg/MDAnalysis.egg-info/PKG-INFO 2021-07-10T11:35:04,281 writing dependency_links to /tmp/pip-pip-egg-info-r7n6j1sg/MDAnalysis.egg-info/dependency_links.txt 2021-07-10T11:35:04,284 writing requirements to /tmp/pip-pip-egg-info-r7n6j1sg/MDAnalysis.egg-info/requires.txt 2021-07-10T11:35:04,285 writing top-level names to /tmp/pip-pip-egg-info-r7n6j1sg/MDAnalysis.egg-info/top_level.txt 2021-07-10T11:35:04,287 writing manifest file '/tmp/pip-pip-egg-info-r7n6j1sg/MDAnalysis.egg-info/SOURCES.txt' 2021-07-10T11:35:04,513 reading manifest file '/tmp/pip-pip-egg-info-r7n6j1sg/MDAnalysis.egg-info/SOURCES.txt' 2021-07-10T11:35:04,516 reading manifest template 'MANIFEST.in' 2021-07-10T11:35:04,582 warning: no files found matching '*.pxd' anywhere in distribution 2021-07-10T11:35:04,586 warning: no files found matching 'MDAnalysis/lib/src/pyqcprot/*' 2021-07-10T11:35:04,678 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-10T11:35:04,680 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2021-07-10T11:35:04,682 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2021-07-10T11:35:04,684 warning: no previously-included files matching '*~' found anywhere in distribution 2021-07-10T11:35:04,685 adding license file 'LICENSE' 2021-07-10T11:35:04,685 adding license file 'AUTHORS' 2021-07-10T11:35:04,702 writing manifest file '/tmp/pip-pip-egg-info-r7n6j1sg/MDAnalysis.egg-info/SOURCES.txt' 2021-07-10T11:35:05,144 Source in /tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356 has version 0.13.0, which satisfies requirement mdanalysis==0.13.0 from https://files.pythonhosted.org/packages/78/33/704a708797267b35bfe27cc40e83eedabad62c7bb143babbc728ee285082/MDAnalysis-0.13.0.tar.gz#sha256=bdf5a15842bd4e4635fcb60297978252c55c5828c9b7003d810c9e19a4fffbe6 2021-07-10T11:35:05,145 Removed mdanalysis==0.13.0 from https://files.pythonhosted.org/packages/78/33/704a708797267b35bfe27cc40e83eedabad62c7bb143babbc728ee285082/MDAnalysis-0.13.0.tar.gz#sha256=bdf5a15842bd4e4635fcb60297978252c55c5828c9b7003d810c9e19a4fffbe6 from build tracker '/tmp/pip-req-tracker-s6dsc3z7' 2021-07-10T11:35:05,150 Created temporary directory: /tmp/pip-unpack-6w8dv9pc 2021-07-10T11:35:05,150 Building wheels for collected packages: mdanalysis 2021-07-10T11:35:05,154 Created temporary directory: /tmp/pip-wheel-ik8us3mw 2021-07-10T11:35:05,155 Building wheel for mdanalysis (setup.py): started 2021-07-10T11:35:05,155 Destination directory: /tmp/pip-wheel-ik8us3mw 2021-07-10T11:35:05,155 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/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-ik8us3mw 2021-07-10T11:35:06,097 /tmp/pip-wheel-cct7jbri/mdanalysis_d0add9f0f5104f9dba59648e55ea2356/setup.py:103: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. 2021-07-10T11:35:06,097 self.config = configparser.SafeConfigParser() 2021-07-10T11:35:06,328 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-10T11:35:07,359 running bdist_wheel 2021-07-10T11:35:07,361 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2021-07-10T11:35:07,364 running build 2021-07-10T11:35:07,364 running build_py 2021-07-10T11:35:07,499 creating build 2021-07-10T11:35:07,499 creating build/lib.linux-armv7l-3.9 2021-07-10T11:35:07,500 creating build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-10T11:35:07,501 copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-10T11:35:07,503 copying MDAnalysis/KDTree.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-10T11:35:07,505 copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-10T11:35:07,508 copying MDAnalysis/version.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-10T11:35:07,509 copying MDAnalysis/units.py -> build/lib.linux-armv7l-3.9/MDAnalysis 2021-07-10T11:35:07,513 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,514 copying MDAnalysis/analysis/helanal.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,517 copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,521 copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,524 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,527 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,530 copying MDAnalysis/analysis/hole.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,534 copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,536 copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,541 copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,545 copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,549 copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,552 copying MDAnalysis/analysis/x3dna.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,556 copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,560 copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,563 copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,567 copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,571 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis 2021-07-10T11:35:07,576 creating build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,578 copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,581 copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,584 copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,586 copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,589 copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,591 copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,594 copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,596 copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,599 copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,602 copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,604 copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,607 copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,609 copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,612 copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,615 copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,617 copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,620 copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,623 copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,625 copying MDAnalysis/topology/PrimitivePDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,628 copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,631 copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology 2021-07-10T11:35:07,634 creating build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-10T11:35:07,635 copying MDAnalysis/migration/test_dummy_torsion.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-10T11:35:07,637 copying MDAnalysis/migration/ten2eleven.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-10T11:35:07,640 copying MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-10T11:35:07,642 copying MDAnalysis/migration/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration 2021-07-10T11:35:07,646 creating build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,647 copying MDAnalysis/core/Selection.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,651 copying MDAnalysis/core/transformations.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,653 copying MDAnalysis/core/parallel.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,655 copying MDAnalysis/core/log.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,658 copying MDAnalysis/core/qcprot.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,660 copying MDAnalysis/core/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,662 copying MDAnalysis/core/Timeseries.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,665 copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,668 copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,671 copying MDAnalysis/core/AtomGroup.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,678 copying MDAnalysis/core/units.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,681 copying MDAnalysis/core/util.py -> build/lib.linux-armv7l-3.9/MDAnalysis/core 2021-07-10T11:35:07,684 creating build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-10T11:35:07,685 copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-10T11:35:07,687 copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/tests 2021-07-10T11:35:07,691 creating build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-10T11:35:07,692 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-10T11:35:07,695 copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-10T11:35:07,699 copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/visualization 2021-07-10T11:35:07,702 creating build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:07,703 copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:07,708 copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:07,710 copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:07,713 copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:07,717 copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:07,719 copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:07,722 copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:07,727 creating build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-10T11:35:07,729 copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-10T11:35:07,731 copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-10T11:35:07,734 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-10T11:35:07,736 copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-10T11:35:07,739 copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-10T11:35:07,741 copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-10T11:35:07,744 copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-3.9/MDAnalysis/selections 2021-07-10T11:35:07,748 creating build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,749 copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,752 copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,755 copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,758 copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,761 copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,764 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,767 copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,769 copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,772 copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,774 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,777 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,780 copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,783 copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,787 copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,790 copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,793 copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,796 copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,801 copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,805 copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,809 copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,813 creating build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-10T11:35:07,814 copying MDAnalysis/analysis/hbonds/hbond_analysis.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-10T11:35:07,819 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-10T11:35:07,821 copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds 2021-07-10T11:35:07,825 creating build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-10T11:35:07,826 copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-10T11:35:07,830 copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-10T11:35:07,832 copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-10T11:35:07,835 copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr 2021-07-10T11:35:07,839 creating build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,840 copying MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,843 copying MDAnalysis/migration/fixes/fix_agmethods2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,845 copying MDAnalysis/migration/fixes/fix_torsions.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,847 copying MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,850 copying MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,852 copying MDAnalysis/migration/fixes/fix_writer.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,854 copying MDAnalysis/migration/fixes/fix_agmethods.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,856 copying MDAnalysis/migration/fixes/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,858 copying MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,861 copying MDAnalysis/migration/fixes/fix_calctorsions.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,863 copying MDAnalysis/migration/fixes/fix_camelcase.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,865 copying MDAnalysis/migration/fixes/fix_mdaimports.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,867 copying MDAnalysis/migration/fixes/fix_numframes.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,869 copying MDAnalysis/migration/fixes/fix_selectatoms.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,871 copying MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes 2021-07-10T11:35:07,874 creating build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:07,875 copying MDAnalysis/coordinates/xdrfile/core.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:07,879 copying MDAnalysis/coordinates/xdrfile/TRR.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:07,882 copying MDAnalysis/coordinates/xdrfile/XTC.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:07,885 copying MDAnalysis/coordinates/xdrfile/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:07,887 copying MDAnalysis/coordinates/xdrfile/statno.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:07,889 copying MDAnalysis/coordinates/xdrfile/libxdrfile2.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:07,893 creating build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/pdb 2021-07-10T11:35:07,894 copying MDAnalysis/coordinates/pdb/extensions.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/pdb 2021-07-10T11:35:07,897 copying MDAnalysis/coordinates/pdb/__init__.py -> build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/pdb 2021-07-10T11:35:07,915 running build_ext 2021-07-10T11:35:07,924 building 'coordinates._dcdmodule' extension 2021-07-10T11:35:07,924 creating build/temp.linux-armv7l-3.9 2021-07-10T11:35:07,925 creating build/temp.linux-armv7l-3.9/MDAnalysis 2021-07-10T11:35:07,926 creating build/temp.linux-armv7l-3.9/MDAnalysis/coordinates 2021-07-10T11:35:07,927 creating build/temp.linux-armv7l-3.9/MDAnalysis/coordinates/src 2021-07-10T11:35:07,928 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 -IMDAnalysis/coordinates/include -I/usr/include/python3.9 -c MDAnalysis/coordinates/src/dcd.c -o build/temp.linux-armv7l-3.9/MDAnalysis/coordinates/src/dcd.o 2021-07-10T11:35:08,346 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-10T11:35:08,346 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-10T11:35:08,346 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-10T11:35:08,346 from MDAnalysis/coordinates/src/dcd.c:22: 2021-07-10T11:35:08,346 /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] 2021-07-10T11:35:08,347 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-10T11:35:08,347 | ^~~~~~~ 2021-07-10T11:35:08,399 In file included from MDAnalysis/coordinates/src/dcd.c:24: 2021-07-10T11:35:08,400 MDAnalysis/coordinates/include/readdcd.h: In function ‘read_dcdstep’: 2021-07-10T11:35:08,400 MDAnalysis/coordinates/include/readdcd.h:561:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T11:35:08,400 561 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-10T11:35:08,400 | ^~ 2021-07-10T11:35:08,414 MDAnalysis/coordinates/src/dcd.c: In function ‘__write_dcd_header’: 2021-07-10T11:35:08,414 MDAnalysis/coordinates/src/dcd.c:90:8: warning: implicit declaration of function ‘PyFile_CheckExact’; did you mean ‘PyType_CheckExact’? [-Wimplicit-function-declaration] 2021-07-10T11:35:08,415 90 | if (!PyFile_CheckExact(temp)) { 2021-07-10T11:35:08,415 | ^~~~~~~~~~~~~~~~~ 2021-07-10T11:35:08,415 | PyType_CheckExact 2021-07-10T11:35:08,423 MDAnalysis/coordinates/src/dcd.c:96:15: warning: implicit declaration of function ‘PyFile_AsFile’ [-Wimplicit-function-declaration] 2021-07-10T11:35:08,424 96 | fd = fileno(PyFile_AsFile(temp)); 2021-07-10T11:35:08,424 | ^~~~~~~~~~~~~ 2021-07-10T11:35:08,424 MDAnalysis/coordinates/src/dcd.c:96:15: warning: passing argument 1 of ‘fileno’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:08,424 96 | fd = fileno(PyFile_AsFile(temp)); 2021-07-10T11:35:08,424 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:08,424 | | 2021-07-10T11:35:08,424 | int 2021-07-10T11:35:08,425 In file included from /usr/include/python3.9/Python.h:25, 2021-07-10T11:35:08,425 from MDAnalysis/coordinates/src/dcd.c:21: 2021-07-10T11:35:08,425 /usr/include/stdio.h:786:26: note: expected ‘FILE *’ but argument is of type ‘int’ 2021-07-10T11:35:08,425 786 | extern int fileno (FILE *__stream) __THROW __wur; 2021-07-10T11:35:08,425 | ~~~~~~^~~~~~~~ 2021-07-10T11:35:08,437 MDAnalysis/coordinates/src/dcd.c:117:10: warning: implicit declaration of function ‘PyCObject_FromVoidPtr’; did you mean ‘PyLong_FromVoidPtr’? [-Wimplicit-function-declaration] 2021-07-10T11:35:08,437 117 | temp = PyCObject_FromVoidPtr(dcd, free); // Creates a New Reference 2021-07-10T11:35:08,437 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:08,438 | PyLong_FromVoidPtr 2021-07-10T11:35:08,438 MDAnalysis/coordinates/src/dcd.c:117:8: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:08,438 117 | temp = PyCObject_FromVoidPtr(dcd, free); // Creates a New Reference 2021-07-10T11:35:08,438 | ^ 2021-07-10T11:35:08,450 MDAnalysis/coordinates/src/dcd.c:127:10: warning: implicit declaration of function ‘PyBuffer_FromMemory’ [-Wimplicit-function-declaration] 2021-07-10T11:35:08,450 127 | temp = PyBuffer_FromMemory(dcd, sizeof(dcdhandle)); // Creates a New Reference 2021-07-10T11:35:08,451 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:08,451 MDAnalysis/coordinates/src/dcd.c:127:8: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:08,451 127 | temp = PyBuffer_FromMemory(dcd, sizeof(dcdhandle)); // Creates a New Reference 2021-07-10T11:35:08,451 | ^ 2021-07-10T11:35:08,463 MDAnalysis/coordinates/src/dcd.c: In function ‘__write_next_frame’: 2021-07-10T11:35:08,463 MDAnalysis/coordinates/src/dcd.c:168:21: warning: implicit declaration of function ‘PyCObject_AsVoidPtr’; did you mean ‘PyLong_AsVoidPtr’? [-Wimplicit-function-declaration] 2021-07-10T11:35:08,464 168 | dcd = (dcdhandle*)PyCObject_AsVoidPtr(temp); 2021-07-10T11:35:08,464 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:08,464 | PyLong_AsVoidPtr 2021-07-10T11:35:08,465 MDAnalysis/coordinates/src/dcd.c: In function ‘__read_dcd_header’: 2021-07-10T11:35:08,465 MDAnalysis/coordinates/src/dcd.c:282:15: warning: passing argument 1 of ‘fileno’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:08,465 282 | fd = fileno(PyFile_AsFile(temp)); 2021-07-10T11:35:08,466 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:08,466 | | 2021-07-10T11:35:08,466 | int 2021-07-10T11:35:08,466 In file included from /usr/include/python3.9/Python.h:25, 2021-07-10T11:35:08,466 from MDAnalysis/coordinates/src/dcd.c:21: 2021-07-10T11:35:08,466 /usr/include/stdio.h:786:26: note: expected ‘FILE *’ but argument is of type ‘int’ 2021-07-10T11:35:08,466 786 | extern int fileno (FILE *__stream) __THROW __wur; 2021-07-10T11:35:08,466 | ~~~~~~^~~~~~~~ 2021-07-10T11:35:08,468 MDAnalysis/coordinates/src/dcd.c:388:8: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:08,468 388 | temp = PyCObject_FromVoidPtr(dcd, NULL); 2021-07-10T11:35:08,468 | ^ 2021-07-10T11:35:08,468 MDAnalysis/coordinates/src/dcd.c:409:8: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:08,469 409 | temp = PyBuffer_FromMemory(dcd, sizeof(dcdhandle)); 2021-07-10T11:35:08,469 | ^ 2021-07-10T11:35:08,477 MDAnalysis/coordinates/src/dcd.c: In function ‘__read_timeseries’: 2021-07-10T11:35:08,477 MDAnalysis/coordinates/src/dcd.c:491:19: warning: implicit declaration of function ‘PyInt_AsLong’; did you mean ‘PyLong_AsLong’? [-Wimplicit-function-declaration] 2021-07-10T11:35:08,477 491 | atomlist[i] = PyInt_AsLong(temp); 2021-07-10T11:35:08,478 | ^~~~~~~~~~~~ 2021-07-10T11:35:08,478 | PyLong_AsLong 2021-07-10T11:35:08,486 MDAnalysis/coordinates/src/dcd.c: In function ‘__reset_dcd_read’: 2021-07-10T11:35:08,487 MDAnalysis/coordinates/src/dcd.c:892:7: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable] 2021-07-10T11:35:08,487 892 | int rc; 2021-07-10T11:35:08,487 | ^~ 2021-07-10T11:35:08,495 MDAnalysis/coordinates/src/dcd.c: In function ‘init_dcdmodule’: 2021-07-10T11:35:08,496 MDAnalysis/coordinates/src/dcd.c:943:10: warning: implicit declaration of function ‘Py_InitModule’ [-Wimplicit-function-declaration] 2021-07-10T11:35:08,496 943 | (void) Py_InitModule("_dcdmodule", DCDMethods); 2021-07-10T11:35:08,496 | ^~~~~~~~~~~~~ 2021-07-10T11:35:08,501 MDAnalysis/coordinates/src/dcd.c:945:1: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-10T11:35:08,502 945 | } 2021-07-10T11:35:08,502 | ^ 2021-07-10T11:35:08,520 In file included from MDAnalysis/coordinates/src/dcd.c:24: 2021-07-10T11:35:08,521 At top level: 2021-07-10T11:35:08,521 MDAnalysis/coordinates/include/readdcd.h:626:12: warning: ‘jump_to_dcdstep’ defined but not used [-Wunused-function] 2021-07-10T11:35:08,521 626 | static int jump_to_dcdstep(fio_fd fd, int natoms, int nsets, int nfixed, int charmm, int header_size, int step) { 2021-07-10T11:35:08,521 | ^~~~~~~~~~~~~~~ 2021-07-10T11:35:08,521 In file included from MDAnalysis/coordinates/include/readdcd.h:26, 2021-07-10T11:35:08,522 from MDAnalysis/coordinates/src/dcd.c:24: 2021-07-10T11:35:08,522 MDAnalysis/coordinates/include/fastio.h:450:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-10T11:35:08,522 450 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-10T11:35:08,522 | ^~~~~~~~~~~~~ 2021-07-10T11:35:08,522 MDAnalysis/coordinates/include/fastio.h:446:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-10T11:35:08,522 446 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-10T11:35:08,522 | ^~~~~~~~~~~~~~ 2021-07-10T11:35:08,522 MDAnalysis/coordinates/include/fastio.h:370:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2021-07-10T11:35:08,523 370 | static int fio_fclose(fio_fd fd) { 2021-07-10T11:35:08,523 | ^~~~~~~~~~ 2021-07-10T11:35:08,523 MDAnalysis/coordinates/include/fastio.h:351:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2021-07-10T11:35:08,523 351 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2021-07-10T11:35:08,523 | ^~~~~~~~ 2021-07-10T11:35:08,524 In file included from MDAnalysis/coordinates/include/readdcd.h:25, 2021-07-10T11:35:08,524 from MDAnalysis/coordinates/src/dcd.c:24: 2021-07-10T11:35:08,524 MDAnalysis/coordinates/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2021-07-10T11:35:08,524 96 | static void swap2_aligned(void *v, long ndata) { 2021-07-10T11:35:08,524 | ^~~~~~~~~~~~~ 2021-07-10T11:35:08,524 MDAnalysis/coordinates/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2021-07-10T11:35:08,525 32 | static void swap2_unaligned(void *v, long ndata) { 2021-07-10T11:35:08,525 | ^~~~~~~~~~~~~~~ 2021-07-10T11:35:10,311 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/coordinates/src/dcd.o -o build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/_dcdmodule.cpython-39-arm-linux-gnueabihf.so 2021-07-10T11:35:10,426 building 'coordinates.dcdtimeseries' extension 2021-07-10T11:35:10,427 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 -IMDAnalysis/coordinates/include -I/usr/include/python3.9 -c MDAnalysis/coordinates/dcdtimeseries.c -o build/temp.linux-armv7l-3.9/MDAnalysis/coordinates/dcdtimeseries.o 2021-07-10T11:35:10,819 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-10T11:35:10,819 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-10T11:35:10,819 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-10T11:35:10,819 from MDAnalysis/coordinates/dcdtimeseries.c:637: 2021-07-10T11:35:10,820 /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] 2021-07-10T11:35:10,820 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-10T11:35:10,820 | ^~~~~~~ 2021-07-10T11:35:10,881 In file included from MDAnalysis/coordinates/dcdtimeseries.c:645: 2021-07-10T11:35:10,882 MDAnalysis/coordinates/include/readdcd.h: In function ‘read_dcdstep’: 2021-07-10T11:35:10,882 MDAnalysis/coordinates/include/readdcd.h:561:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T11:35:10,882 561 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-10T11:35:10,882 | ^~ 2021-07-10T11:35:10,920 MDAnalysis/coordinates/dcdtimeseries.c: In function ‘__pyx_pf_11coordinates_13dcdtimeseries___read_timecorrel’: 2021-07-10T11:35:10,921 MDAnalysis/coordinates/dcdtimeseries.c:2028:69: warning: implicit declaration of function ‘PyCObject_AsVoidPtr’; did you mean ‘PyLong_AsVoidPtr’? [-Wimplicit-function-declaration] 2021-07-10T11:35:10,922 2028 | __pyx_v_dcd = ((__pyx_t_11coordinates_13dcdtimeseries_dcdhandle *)PyCObject_AsVoidPtr(__pyx_t_1)); 2021-07-10T11:35:10,922 | ^~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:10,922 | PyLong_AsVoidPtr 2021-07-10T11:35:10,936 MDAnalysis/coordinates/dcdtimeseries.c:2111:20: warning: implicit declaration of function ‘PyString_AsString’ [-Wimplicit-function-declaration] 2021-07-10T11:35:10,936 2111 | __pyx_v_fmtstr = PyString_AsString(__pyx_v_format); 2021-07-10T11:35:10,936 | ^~~~~~~~~~~~~~~~~ 2021-07-10T11:35:10,937 MDAnalysis/coordinates/dcdtimeseries.c:2111:18: warning: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:10,937 2111 | __pyx_v_fmtstr = PyString_AsString(__pyx_v_format); 2021-07-10T11:35:10,937 | ^ 2021-07-10T11:35:11,184 In file included from MDAnalysis/coordinates/dcdtimeseries.c:645: 2021-07-10T11:35:11,184 At top level: 2021-07-10T11:35:11,184 MDAnalysis/coordinates/include/readdcd.h:758:13: warning: ‘close_dcd_read’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,184 758 | static void close_dcd_read(int *indexes, float *fixedcoords) { 2021-07-10T11:35:11,184 | ^~~~~~~~~~~~~~ 2021-07-10T11:35:11,184 MDAnalysis/coordinates/include/readdcd.h:690:12: warning: ‘write_dcdheader’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,185 690 | static int write_dcdheader(fio_fd fd, const char *remarks, int N, 2021-07-10T11:35:11,185 | ^~~~~~~~~~~~~~~ 2021-07-10T11:35:11,185 MDAnalysis/coordinates/include/readdcd.h:653:12: warning: ‘write_dcdstep’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,185 653 | static int write_dcdstep(fio_fd fd, int curframe, int curstep, int N, 2021-07-10T11:35:11,185 | ^~~~~~~~~~~~~ 2021-07-10T11:35:11,185 MDAnalysis/coordinates/include/readdcd.h:502:12: warning: ‘read_dcdstep’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,185 502 | static int read_dcdstep(fio_fd fd, int N, float *X, float *Y, float *Z, 2021-07-10T11:35:11,185 | ^~~~~~~~~~~~ 2021-07-10T11:35:11,186 In file included from MDAnalysis/coordinates/dcdtimeseries.c:645: 2021-07-10T11:35:11,186 MDAnalysis/coordinates/include/readdcd.h:169:12: warning: ‘read_dcdheader’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,186 169 | static int read_dcdheader(fio_fd fd, int *N, int *NSET, int *ISTART, 2021-07-10T11:35:11,186 | ^~~~~~~~~~~~~~ 2021-07-10T11:35:11,186 In file included from MDAnalysis/coordinates/include/readdcd.h:26, 2021-07-10T11:35:11,186 from MDAnalysis/coordinates/dcdtimeseries.c:645: 2021-07-10T11:35:11,186 MDAnalysis/coordinates/include/fastio.h:450:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,187 450 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-10T11:35:11,187 | ^~~~~~~~~~~~~ 2021-07-10T11:35:11,187 MDAnalysis/coordinates/include/fastio.h:446:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,187 446 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-10T11:35:11,187 | ^~~~~~~~~~~~~~ 2021-07-10T11:35:11,187 MDAnalysis/coordinates/include/fastio.h:433:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,187 433 | static fio_size_t fio_ftell(fio_fd fd) { 2021-07-10T11:35:11,187 | ^~~~~~~~~ 2021-07-10T11:35:11,188 MDAnalysis/coordinates/include/fastio.h:370:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,188 370 | static int fio_fclose(fio_fd fd) { 2021-07-10T11:35:11,188 | ^~~~~~~~~~ 2021-07-10T11:35:11,188 MDAnalysis/coordinates/include/fastio.h:351:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,188 351 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2021-07-10T11:35:11,188 | ^~~~~~~~ 2021-07-10T11:35:11,188 In file included from MDAnalysis/coordinates/include/readdcd.h:25, 2021-07-10T11:35:11,189 from MDAnalysis/coordinates/dcdtimeseries.c:645: 2021-07-10T11:35:11,189 MDAnalysis/coordinates/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,189 96 | static void swap2_aligned(void *v, long ndata) { 2021-07-10T11:35:11,189 | ^~~~~~~~~~~~~ 2021-07-10T11:35:11,189 MDAnalysis/coordinates/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2021-07-10T11:35:11,190 32 | static void swap2_unaligned(void *v, long ndata) { 2021-07-10T11:35:11,190 | ^~~~~~~~~~~~~~~ 2021-07-10T11:35:15,764 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/coordinates/dcdtimeseries.o -o build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/dcdtimeseries.cpython-39-arm-linux-gnueabihf.so 2021-07-10T11:35:15,894 building 'lib.c_distances' extension 2021-07-10T11:35:15,895 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib 2021-07-10T11:35:15,895 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 -IMDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/c_distances.o 2021-07-10T11:35:16,285 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-10T11:35:16,286 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-10T11:35:16,286 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-10T11:35:16,286 from MDAnalysis/lib/c_distances.c:639: 2021-07-10T11:35:16,286 /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] 2021-07-10T11:35:16,286 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-10T11:35:16,286 | ^~~~~~~ 2021-07-10T11:35:31,581 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 2021-07-10T11:35:31,773 building 'lib.c_distances_openmp' extension 2021-07-10T11:35:31,773 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPARALLEL -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -IMDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-armv7l-3.9/MDAnalysis/lib/c_distances_openmp.o -fopenmp 2021-07-10T11:35:32,160 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-10T11:35:32,160 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-10T11:35:32,160 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-10T11:35:32,160 from MDAnalysis/lib/c_distances_openmp.c:652: 2021-07-10T11:35:32,160 /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] 2021-07-10T11:35:32,161 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-10T11:35:32,161 | ^~~~~~~ 2021-07-10T11:35:36,529 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 2021-07-10T11:35:36,684 building 'lib.qcprot' extension 2021-07-10T11:35:36,685 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 -O3 -ffast-math 2021-07-10T11:35:37,060 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-10T11:35:37,060 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-10T11:35:37,060 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-10T11:35:37,060 from MDAnalysis/lib/qcprot.c:638: 2021-07-10T11:35:37,060 /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] 2021-07-10T11:35:37,060 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-10T11:35:37,061 | ^~~~~~~ 2021-07-10T11:35:37,125 MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_3lib_6qcprot_InnerProduct’: 2021-07-10T11:35:37,125 MDAnalysis/lib/qcprot.c:2205:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:37,126 2205 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2021-07-10T11:35:37,126 | ^ 2021-07-10T11:35:37,129 MDAnalysis/lib/qcprot.c:2413:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:37,129 2413 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2021-07-10T11:35:37,129 | ^ 2021-07-10T11:35:41,417 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 2021-07-10T11:35:41,545 building 'lib._transformations' extension 2021-07-10T11:35:41,545 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/src 2021-07-10T11:35:41,546 creating build/temp.linux-armv7l-3.9/MDAnalysis/lib/src/transformations 2021-07-10T11:35:41,546 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 2021-07-10T11:35:41,934 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-10T11:35:41,934 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-10T11:35:41,934 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-10T11:35:41,934 from MDAnalysis/lib/src/transformations/transformations.c:73: 2021-07-10T11:35:41,934 /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] 2021-07-10T11:35:41,934 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-10T11:35:41,935 | ^~~~~~~ 2021-07-10T11:35:42,000 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: 2021-07-10T11:35:42,001 MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,001 1845 | #pragma vector always 2021-07-10T11:35:42,001 | 2021-07-10T11:35:42,004 MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,004 1962 | #pragma vector always 2021-07-10T11:35:42,005 | 2021-07-10T11:35:42,005 MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,005 1986 | #pragma vector always 2021-07-10T11:35:42,005 | 2021-07-10T11:35:42,008 MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: 2021-07-10T11:35:42,009 MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] 2021-07-10T11:35:42,010 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { 2021-07-10T11:35:42,010 | ^~ 2021-07-10T11:35:42,010 In file included from /usr/include/python3.9/Python.h:97, 2021-07-10T11:35:42,010 from MDAnalysis/lib/src/transformations/transformations.c:68: 2021-07-10T11:35:42,010 /usr/include/python3.9/unicodeobject.h:177:43: note: declared here 2021-07-10T11:35:42,011 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( 2021-07-10T11:35:42,011 | ^~~~~~~~~~~~~~~~~ 2021-07-10T11:35:42,045 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: 2021-07-10T11:35:42,045 MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,045 3427 | #pragma vector always 2021-07-10T11:35:42,045 | 2021-07-10T11:35:42,047 MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,048 3508 | #pragma vector always 2021-07-10T11:35:42,048 | 2021-07-10T11:35:42,053 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: 2021-07-10T11:35:42,053 MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,053 3610 | #pragma vector always 2021-07-10T11:35:42,053 | 2021-07-10T11:35:42,054 MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,054 3615 | #pragma vector always 2021-07-10T11:35:42,054 | 2021-07-10T11:35:42,059 MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,059 3679 | #pragma vector always 2021-07-10T11:35:42,059 | 2021-07-10T11:35:42,059 MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2021-07-10T11:35:42,059 3684 | #pragma vector always 2021-07-10T11:35:42,059 | 2021-07-10T11:35:42,129 At top level: 2021-07-10T11:35:42,130 MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] 2021-07-10T11:35:42,130 910 | PyConverter_DoubleVector4Copy( 2021-07-10T11:35:42,130 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:42,130 MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] 2021-07-10T11:35:42,130 804 | PyConverter_DoubleArrayOrNone( 2021-07-10T11:35:42,130 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:42,130 MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] 2021-07-10T11:35:42,131 774 | PyConverter_DoubleArray( 2021-07-10T11:35:42,131 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:46,480 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 2021-07-10T11:35:46,617 building 'coordinates.xdrfile._libxdrfile2' extension 2021-07-10T11:35:46,618 creating build/temp.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:46,618 creating build/temp.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/src 2021-07-10T11:35:46,619 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c -o build/temp.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.o 2021-07-10T11:35:47,046 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-10T11:35:47,047 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-10T11:35:47,047 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-10T11:35:47,047 from MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:2992: 2021-07-10T11:35:47,047 /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] 2021-07-10T11:35:47,047 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-10T11:35:47,047 | ^~~~~~~ 2021-07-10T11:35:47,088 MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c: In function ‘my_read_xtc_n_frames’: 2021-07-10T11:35:47,091 MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:3125:31: warning: implicit declaration of function ‘PyCObject_FromVoidPtr’; did you mean ‘PyLong_FromVoidPtr’? [-Wimplicit-function-declaration] 2021-07-10T11:35:47,091 3125 | PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free); 2021-07-10T11:35:47,092 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:47,092 | PyLong_FromVoidPtr 2021-07-10T11:35:47,093 MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:3125:29: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:47,093 3125 | PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free); 2021-07-10T11:35:47,093 | ^ 2021-07-10T11:35:47,094 MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c: In function ‘my_read_trr_n_frames’: 2021-07-10T11:35:47,095 MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:3164:29: warning: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2021-07-10T11:35:47,096 3164 | PyArray_BASE(npoffsets) = PyCObject_FromVoidPtr(*offsets, free); 2021-07-10T11:35:47,096 | ^ 2021-07-10T11:35:47,109 MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c: In function ‘pytype_string’: 2021-07-10T11:35:47,112 MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:3264:9: warning: implicit declaration of function ‘PyFile_Check’; did you mean ‘PyCell_Check’? [-Wimplicit-function-declaration] 2021-07-10T11:35:47,112 3264 | if (PyFile_Check( py_obj)) return "file" ; 2021-07-10T11:35:47,112 | ^~~~~~~~~~~~ 2021-07-10T11:35:47,112 | PyCell_Check 2021-07-10T11:35:47,125 MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:3266:9: warning: implicit declaration of function ‘PyInstance_Check’; did you mean ‘PySequence_Check’? [-Wimplicit-function-declaration] 2021-07-10T11:35:47,125 3266 | if (PyInstance_Check(py_obj)) return "instance" ; 2021-07-10T11:35:47,126 | ^~~~~~~~~~~~~~~~ 2021-07-10T11:35:47,126 | PySequence_Check 2021-07-10T11:35:48,775 In file included from /usr/include/string.h:495, 2021-07-10T11:35:48,776 from /usr/include/python3.9/Python.h:30, 2021-07-10T11:35:48,776 from MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:125: 2021-07-10T11:35:48,776 In function ‘strncpy’, 2021-07-10T11:35:48,776 inlined from ‘SWIG_Python_FixMethods’ at MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:5064:15, 2021-07-10T11:35:48,776 inlined from ‘PyInit__libxdrfile2’ at MDAnalysis/coordinates/xdrfile/src/libxdrfile2_wrap.c:5162:3: 2021-07-10T11:35:48,776 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 10 bytes from a string of the same length [-Wstringop-truncation] 2021-07-10T11:35:48,777 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-10T11:35:48,777 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T11:35:49,274 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/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/coordinates/xdrfile/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/src/xdrfile.o 2021-07-10T11:35:49,439 MDAnalysis/coordinates/xdrfile/src/xdrfile.c: In function ‘sizeofint’: 2021-07-10T11:35:49,439 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:490:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T11:35:49,439 490 | while (size >= num && num_of_bits < 32) 2021-07-10T11:35:49,440 | ^~ 2021-07-10T11:35:49,440 MDAnalysis/coordinates/xdrfile/src/xdrfile.c: In function ‘sizeofints’: 2021-07-10T11:35:49,440 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:536:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:49,440 536 | while (bytes[num_of_bytes] >= num) 2021-07-10T11:35:49,440 | ^~ 2021-07-10T11:35:49,441 MDAnalysis/coordinates/xdrfile/src/xdrfile.c: In function ‘encodeints’: 2021-07-10T11:35:49,441 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:645:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T11:35:49,441 645 | if (num_of_bits >= num_of_bytes * 8) 2021-07-10T11:35:49,441 | ^~ 2021-07-10T11:35:49,442 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:647:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T11:35:49,442 647 | for (i = 0; i < num_of_bytes; i++) 2021-07-10T11:35:49,442 | ^ 2021-07-10T11:35:49,442 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:655:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T11:35:49,442 655 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-10T11:35:49,442 | ^ 2021-07-10T11:35:49,443 MDAnalysis/coordinates/xdrfile/src/xdrfile.c: In function ‘decodebits’: 2021-07-10T11:35:49,443 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:695:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:49,443 695 | if (lastbits < num_of_bits) 2021-07-10T11:35:49,443 | ^ 2021-07-10T11:35:49,444 MDAnalysis/coordinates/xdrfile/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-10T11:35:49,444 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:805:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:49,445 805 | if(size3>xfp->buf1size) 2021-07-10T11:35:49,445 | ^ 2021-07-10T11:35:49,446 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:857:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:49,446 857 | maxidx = (LASTIDXxfp->buf1size) 2021-07-10T11:35:49,451 | ^ 2021-07-10T11:35:49,455 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:1124:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T11:35:49,455 1124 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-10T11:35:49,455 | ^ 2021-07-10T11:35:49,456 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:1130:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:49,456 1130 | maxidx = (LASTIDXxfp->buf1size) 2021-07-10T11:35:49,462 | ^ 2021-07-10T11:35:49,463 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:1357:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:49,463 1357 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-10T11:35:49,469 | ^ 2021-07-10T11:35:49,474 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:1608:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T11:35:49,475 1608 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-10T11:35:49,475 | ^ 2021-07-10T11:35:49,475 MDAnalysis/coordinates/xdrfile/src/xdrfile.c:1613:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T11:35:49,475 1613 | maxidx = (LASTIDX build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-10T11:35:52,924 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-10T11:35:52,927 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2021-07-10T11:35:52,930 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/helanal.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,934 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,938 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,943 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,945 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,948 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,952 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,955 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,959 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,963 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,966 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,968 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,972 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,975 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,978 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,982 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,987 copying build/lib.linux-armv7l-3.9/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2021-07-10T11:35:52,994 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:52,995 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:52,998 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,001 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,004 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,006 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,009 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-10T11:35:53,010 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-10T11:35:53,014 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-10T11:35:53,016 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-10T11:35:53,018 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2021-07-10T11:35:53,022 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,024 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,026 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,028 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,031 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,034 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,037 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,040 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,042 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,045 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,048 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,050 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,053 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,056 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PrimitivePDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,059 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,062 copying build/lib.linux-armv7l-3.9/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2021-07-10T11:35:53,064 creating build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-10T11:35:53,066 creating build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,068 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_framenumberingzerobased.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,070 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_agmethods2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,073 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_torsions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,075 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,077 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_agsetterpluralization.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,079 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_writer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,082 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_agmethods.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,084 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,086 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_torsionclasses.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,089 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_calctorsions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,091 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_camelcase.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,093 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_mdaimports.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,096 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_numframes.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,098 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_selectatoms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,101 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/fixes/fix_agcountmethods.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration/fixes 2021-07-10T11:35:53,103 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/test_dummy_torsion.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-10T11:35:53,104 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/ten2eleven.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-10T11:35:53,107 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/test_dummy_old_MDA_code.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-10T11:35:53,109 copying build/lib.linux-armv7l-3.9/MDAnalysis/migration/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/migration 2021-07-10T11:35:53,112 creating build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,113 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/Selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,116 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,118 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/parallel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,120 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,122 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/qcprot.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,124 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,126 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/Timeseries.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,129 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,132 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,136 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/AtomGroup.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,144 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,147 copying build/lib.linux-armv7l-3.9/MDAnalysis/core/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2021-07-10T11:35:53,149 copying build/lib.linux-armv7l-3.9/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-10T11:35:53,152 copying build/lib.linux-armv7l-3.9/MDAnalysis/KDTree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-10T11:35:53,154 copying build/lib.linux-armv7l-3.9/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-10T11:35:53,157 creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-10T11:35:53,158 copying build/lib.linux-armv7l-3.9/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-10T11:35:53,160 copying build/lib.linux-armv7l-3.9/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2021-07-10T11:35:53,163 creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-10T11:35:53,164 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-10T11:35:53,168 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-10T11:35:53,171 copying build/lib.linux-armv7l-3.9/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2021-07-10T11:35:53,173 copying build/lib.linux-armv7l-3.9/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-10T11:35:53,176 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,177 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,207 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,214 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,225 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,228 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,231 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,234 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 2021-07-10T11:35:53,243 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,247 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,249 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,252 copying build/lib.linux-armv7l-3.9/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2021-07-10T11:35:53,256 creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-10T11:35:53,257 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-10T11:35:53,260 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-10T11:35:53,262 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-10T11:35:53,264 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-10T11:35:53,267 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-10T11:35:53,269 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-10T11:35:53,272 copying build/lib.linux-armv7l-3.9/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2021-07-10T11:35:53,275 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,276 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,279 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,282 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,284 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,287 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,290 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,293 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,295 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,298 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,300 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,303 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,305 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,308 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,312 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:53,313 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:53,317 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:53,320 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:53,323 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/_libxdrfile2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:53,334 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:53,336 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/statno.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:53,339 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/xdrfile/libxdrfile2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/xdrfile 2021-07-10T11:35:53,344 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,347 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,350 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,354 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/pdb 2021-07-10T11:35:53,355 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/pdb/extensions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/pdb 2021-07-10T11:35:53,358 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/pdb/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates/pdb 2021-07-10T11:35:53,360 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,363 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/dcdtimeseries.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,375 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,385 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,398 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/_dcdmodule.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,407 copying build/lib.linux-armv7l-3.9/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2021-07-10T11:35:53,409 copying build/lib.linux-armv7l-3.9/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2021-07-10T11:35:53,413 running install_egg_info 2021-07-10T11:35:53,438 running egg_info 2021-07-10T11:35:53,439 writing MDAnalysis.egg-info/PKG-INFO 2021-07-10T11:35:53,441 writing dependency_links to MDAnalysis.egg-info/dependency_links.txt 2021-07-10T11:35:53,443 writing requirements to MDAnalysis.egg-info/requires.txt 2021-07-10T11:35:53,444 writing top-level names to MDAnalysis.egg-info/top_level.txt 2021-07-10T11:35:53,511 reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2021-07-10T11:35:53,555 reading manifest template 'MANIFEST.in' 2021-07-10T11:35:53,654 warning: no files found matching '*.pxd' anywhere in distribution 2021-07-10T11:35:53,659 warning: no files found matching 'MDAnalysis/lib/src/pyqcprot/*' 2021-07-10T11:35:53,739 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-10T11:35:53,741 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2021-07-10T11:35:53,743 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2021-07-10T11:35:53,745 warning: no previously-included files matching '*~' found anywhere in distribution 2021-07-10T11:35:53,745 adding license file 'LICENSE' 2021-07-10T11:35:53,745 adding license file 'AUTHORS' 2021-07-10T11:35:53,766 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2021-07-10T11:35:53,768 Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-0.13.0-py3.9.egg-info 2021-07-10T11:35:53,783 running install_scripts 2021-07-10T11:35:53,838 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-10T11:35:53,839 adding license file "AUTHORS" (matched pattern "AUTHORS*") 2021-07-10T11:35:53,846 creating build/bdist.linux-armv7l/wheel/MDAnalysis-0.13.0.dist-info/WHEEL 2021-07-10T11:35:53,849 creating '/tmp/pip-wheel-ik8us3mw/MDAnalysis-0.13.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-10T11:35:53,851 adding 'MDAnalysis/KDTree.py' 2021-07-10T11:35:53,853 adding 'MDAnalysis/__init__.py' 2021-07-10T11:35:53,854 adding 'MDAnalysis/exceptions.py' 2021-07-10T11:35:53,856 adding 'MDAnalysis/units.py' 2021-07-10T11:35:53,858 adding 'MDAnalysis/version.py' 2021-07-10T11:35:53,859 adding 'MDAnalysis/analysis/__init__.py' 2021-07-10T11:35:53,865 adding 'MDAnalysis/analysis/align.py' 2021-07-10T11:35:53,867 adding 'MDAnalysis/analysis/base.py' 2021-07-10T11:35:53,871 adding 'MDAnalysis/analysis/contacts.py' 2021-07-10T11:35:53,876 adding 'MDAnalysis/analysis/density.py' 2021-07-10T11:35:53,878 adding 'MDAnalysis/analysis/distances.py' 2021-07-10T11:35:53,880 adding 'MDAnalysis/analysis/gnm.py' 2021-07-10T11:35:53,884 adding 'MDAnalysis/analysis/helanal.py' 2021-07-10T11:35:53,890 adding 'MDAnalysis/analysis/hole.py' 2021-07-10T11:35:53,893 adding 'MDAnalysis/analysis/leaflet.py' 2021-07-10T11:35:53,895 adding 'MDAnalysis/analysis/nuclinfo.py' 2021-07-10T11:35:53,897 adding 'MDAnalysis/analysis/polymer.py' 2021-07-10T11:35:53,906 adding 'MDAnalysis/analysis/psa.py' 2021-07-10T11:35:53,908 adding 'MDAnalysis/analysis/rdf.py' 2021-07-10T11:35:53,911 adding 'MDAnalysis/analysis/rms.py' 2021-07-10T11:35:53,915 adding 'MDAnalysis/analysis/waterdynamics.py' 2021-07-10T11:35:53,919 adding 'MDAnalysis/analysis/x3dna.py' 2021-07-10T11:35:53,921 adding 'MDAnalysis/analysis/hbonds/__init__.py' 2021-07-10T11:35:53,928 adding 'MDAnalysis/analysis/hbonds/hbond_analysis.py' 2021-07-10T11:35:53,931 adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' 2021-07-10T11:35:53,933 adding 'MDAnalysis/coordinates/CRD.py' 2021-07-10T11:35:53,936 adding 'MDAnalysis/coordinates/DCD.py' 2021-07-10T11:35:53,938 adding 'MDAnalysis/coordinates/DLPoly.py' 2021-07-10T11:35:53,939 adding 'MDAnalysis/coordinates/DMS.py' 2021-07-10T11:35:53,941 adding 'MDAnalysis/coordinates/GMS.py' 2021-07-10T11:35:53,943 adding 'MDAnalysis/coordinates/GRO.py' 2021-07-10T11:35:53,945 adding 'MDAnalysis/coordinates/INPCRD.py' 2021-07-10T11:35:53,946 adding 'MDAnalysis/coordinates/LAMMPS.py' 2021-07-10T11:35:53,948 adding 'MDAnalysis/coordinates/MOL2.py' 2021-07-10T11:35:53,954 adding 'MDAnalysis/coordinates/PDB.py' 2021-07-10T11:35:53,957 adding 'MDAnalysis/coordinates/PDBQT.py' 2021-07-10T11:35:53,960 adding 'MDAnalysis/coordinates/PQR.py' 2021-07-10T11:35:53,964 adding 'MDAnalysis/coordinates/TRJ.py' 2021-07-10T11:35:53,965 adding 'MDAnalysis/coordinates/TRR.py' 2021-07-10T11:35:53,968 adding 'MDAnalysis/coordinates/TRZ.py' 2021-07-10T11:35:53,969 adding 'MDAnalysis/coordinates/XTC.py' 2021-07-10T11:35:53,972 adding 'MDAnalysis/coordinates/XYZ.py' 2021-07-10T11:35:53,975 adding 'MDAnalysis/coordinates/__init__.py' 2021-07-10T11:35:53,999 adding 'MDAnalysis/coordinates/_dcdmodule.cpython-39-arm-linux-gnueabihf.so' 2021-07-10T11:35:54,007 adding 'MDAnalysis/coordinates/base.py' 2021-07-10T11:35:54,009 adding 'MDAnalysis/coordinates/core.py' 2021-07-10T11:35:54,071 adding 'MDAnalysis/coordinates/dcdtimeseries.cpython-39-arm-linux-gnueabihf.so' 2021-07-10T11:35:54,075 adding 'MDAnalysis/coordinates/pdb/__init__.py' 2021-07-10T11:35:54,077 adding 'MDAnalysis/coordinates/pdb/extensions.py' 2021-07-10T11:35:54,079 adding 'MDAnalysis/coordinates/xdrfile/TRR.py' 2021-07-10T11:35:54,080 adding 'MDAnalysis/coordinates/xdrfile/XTC.py' 2021-07-10T11:35:54,082 adding 'MDAnalysis/coordinates/xdrfile/__init__.py' 2021-07-10T11:35:54,149 adding 'MDAnalysis/coordinates/xdrfile/_libxdrfile2.cpython-39-arm-linux-gnueabihf.so' 2021-07-10T11:35:54,156 adding 'MDAnalysis/coordinates/xdrfile/core.py' 2021-07-10T11:35:54,158 adding 'MDAnalysis/coordinates/xdrfile/libxdrfile2.py' 2021-07-10T11:35:54,159 adding 'MDAnalysis/coordinates/xdrfile/statno.py' 2021-07-10T11:35:54,182 adding 'MDAnalysis/core/AtomGroup.py' 2021-07-10T11:35:54,188 adding 'MDAnalysis/core/Selection.py' 2021-07-10T11:35:54,190 adding 'MDAnalysis/core/Timeseries.py' 2021-07-10T11:35:54,192 adding 'MDAnalysis/core/__init__.py' 2021-07-10T11:35:54,194 adding 'MDAnalysis/core/distances.py' 2021-07-10T11:35:54,195 adding 'MDAnalysis/core/log.py' 2021-07-10T11:35:54,196 adding 'MDAnalysis/core/parallel.py' 2021-07-10T11:35:54,197 adding 'MDAnalysis/core/qcprot.py' 2021-07-10T11:35:54,201 adding 'MDAnalysis/core/topologyobjects.py' 2021-07-10T11:35:54,203 adding 'MDAnalysis/core/transformations.py' 2021-07-10T11:35:54,204 adding 'MDAnalysis/core/units.py' 2021-07-10T11:35:54,205 adding 'MDAnalysis/core/util.py' 2021-07-10T11:35:54,207 adding 'MDAnalysis/lib/NeighborSearch.py' 2021-07-10T11:35:54,208 adding 'MDAnalysis/lib/__init__.py' 2021-07-10T11:35:54,258 adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so' 2021-07-10T11:35:54,458 adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so' 2021-07-10T11:35:54,513 adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so' 2021-07-10T11:35:54,518 adding 'MDAnalysis/lib/distances.py' 2021-07-10T11:35:54,520 adding 'MDAnalysis/lib/log.py' 2021-07-10T11:35:54,522 adding 'MDAnalysis/lib/mdamath.py' 2021-07-10T11:35:54,578 adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so' 2021-07-10T11:35:54,587 adding 'MDAnalysis/lib/transformations.py' 2021-07-10T11:35:54,594 adding 'MDAnalysis/lib/util.py' 2021-07-10T11:35:54,595 adding 'MDAnalysis/migration/__init__.py' 2021-07-10T11:35:54,596 adding 'MDAnalysis/migration/ten2eleven.py' 2021-07-10T11:35:54,598 adding 'MDAnalysis/migration/test_dummy_old_MDA_code.py' 2021-07-10T11:35:54,599 adding 'MDAnalysis/migration/test_dummy_torsion.py' 2021-07-10T11:35:54,600 adding 'MDAnalysis/migration/fixes/__init__.py' 2021-07-10T11:35:54,602 adding 'MDAnalysis/migration/fixes/fix_agcountmethods.py' 2021-07-10T11:35:54,603 adding 'MDAnalysis/migration/fixes/fix_agmethods.py' 2021-07-10T11:35:54,604 adding 'MDAnalysis/migration/fixes/fix_agmethods2.py' 2021-07-10T11:35:54,605 adding 'MDAnalysis/migration/fixes/fix_agsetterpluralization.py' 2021-07-10T11:35:54,606 adding 'MDAnalysis/migration/fixes/fix_calctorsions.py' 2021-07-10T11:35:54,608 adding 'MDAnalysis/migration/fixes/fix_camelcase.py' 2021-07-10T11:35:54,609 adding 'MDAnalysis/migration/fixes/fix_framenumberingzerobased.py' 2021-07-10T11:35:54,610 adding 'MDAnalysis/migration/fixes/fix_framenumberingzerobased2.py' 2021-07-10T11:35:54,611 adding 'MDAnalysis/migration/fixes/fix_mdaimports.py' 2021-07-10T11:35:54,612 adding 'MDAnalysis/migration/fixes/fix_numframes.py' 2021-07-10T11:35:54,613 adding 'MDAnalysis/migration/fixes/fix_selectatoms.py' 2021-07-10T11:35:54,615 adding 'MDAnalysis/migration/fixes/fix_torsionclasses.py' 2021-07-10T11:35:54,616 adding 'MDAnalysis/migration/fixes/fix_torsions.py' 2021-07-10T11:35:54,617 adding 'MDAnalysis/migration/fixes/fix_writer.py' 2021-07-10T11:35:54,618 adding 'MDAnalysis/selections/__init__.py' 2021-07-10T11:35:54,620 adding 'MDAnalysis/selections/base.py' 2021-07-10T11:35:54,622 adding 'MDAnalysis/selections/charmm.py' 2021-07-10T11:35:54,623 adding 'MDAnalysis/selections/gromacs.py' 2021-07-10T11:35:54,624 adding 'MDAnalysis/selections/jmol.py' 2021-07-10T11:35:54,626 adding 'MDAnalysis/selections/pymol.py' 2021-07-10T11:35:54,627 adding 'MDAnalysis/selections/vmd.py' 2021-07-10T11:35:54,629 adding 'MDAnalysis/tests/__init__.py' 2021-07-10T11:35:54,630 adding 'MDAnalysis/tests/datafiles.py' 2021-07-10T11:35:54,632 adding 'MDAnalysis/topology/CRDParser.py' 2021-07-10T11:35:54,633 adding 'MDAnalysis/topology/DLPolyParser.py' 2021-07-10T11:35:54,635 adding 'MDAnalysis/topology/DMSParser.py' 2021-07-10T11:35:54,636 adding 'MDAnalysis/topology/ExtendedPDBParser.py' 2021-07-10T11:35:54,637 adding 'MDAnalysis/topology/GMSParser.py' 2021-07-10T11:35:54,639 adding 'MDAnalysis/topology/GROParser.py' 2021-07-10T11:35:54,640 adding 'MDAnalysis/topology/HoomdXMLParser.py' 2021-07-10T11:35:54,643 adding 'MDAnalysis/topology/LAMMPSParser.py' 2021-07-10T11:35:54,645 adding 'MDAnalysis/topology/MOL2Parser.py' 2021-07-10T11:35:54,646 adding 'MDAnalysis/topology/PDBParser.py' 2021-07-10T11:35:54,647 adding 'MDAnalysis/topology/PDBQTParser.py' 2021-07-10T11:35:54,649 adding 'MDAnalysis/topology/PQRParser.py' 2021-07-10T11:35:54,651 adding 'MDAnalysis/topology/PSFParser.py' 2021-07-10T11:35:54,652 adding 'MDAnalysis/topology/PrimitivePDBParser.py' 2021-07-10T11:35:54,654 adding 'MDAnalysis/topology/TOPParser.py' 2021-07-10T11:35:54,656 adding 'MDAnalysis/topology/TPRParser.py' 2021-07-10T11:35:54,657 adding 'MDAnalysis/topology/XYZParser.py' 2021-07-10T11:35:54,659 adding 'MDAnalysis/topology/__init__.py' 2021-07-10T11:35:54,661 adding 'MDAnalysis/topology/base.py' 2021-07-10T11:35:54,663 adding 'MDAnalysis/topology/core.py' 2021-07-10T11:35:54,665 adding 'MDAnalysis/topology/tables.py' 2021-07-10T11:35:54,666 adding 'MDAnalysis/topology/tpr/__init__.py' 2021-07-10T11:35:54,668 adding 'MDAnalysis/topology/tpr/obj.py' 2021-07-10T11:35:54,669 adding 'MDAnalysis/topology/tpr/setting.py' 2021-07-10T11:35:54,673 adding 'MDAnalysis/topology/tpr/utils.py' 2021-07-10T11:35:54,675 adding 'MDAnalysis/visualization/__init__.py' 2021-07-10T11:35:54,677 adding 'MDAnalysis/visualization/streamlines.py' 2021-07-10T11:35:54,680 adding 'MDAnalysis/visualization/streamlines_3D.py' 2021-07-10T11:35:54,683 adding 'MDAnalysis-0.13.0.dist-info/AUTHORS' 2021-07-10T11:35:54,687 adding 'MDAnalysis-0.13.0.dist-info/LICENSE' 2021-07-10T11:35:54,688 adding 'MDAnalysis-0.13.0.dist-info/METADATA' 2021-07-10T11:35:54,689 adding 'MDAnalysis-0.13.0.dist-info/WHEEL' 2021-07-10T11:35:54,690 adding 'MDAnalysis-0.13.0.dist-info/pbr.json' 2021-07-10T11:35:54,691 adding 'MDAnalysis-0.13.0.dist-info/top_level.txt' 2021-07-10T11:35:54,693 adding 'MDAnalysis-0.13.0.dist-info/RECORD' 2021-07-10T11:35:54,722 removing build/bdist.linux-armv7l/wheel 2021-07-10T11:35:54,922 Building wheel for mdanalysis (setup.py): finished with status 'done' 2021-07-10T11:35:54,943 Created wheel for mdanalysis: filename=MDAnalysis-0.13.0-cp39-cp39-linux_armv7l.whl size=1481571 sha256=ef25ee9269f3b7f8ab95f1c3c563c39740fd2b7801df49d6be7e702c7db7f8fc 2021-07-10T11:35:54,944 Stored in directory: /tmp/pip-ephem-wheel-cache-ykpl05dh/wheels/d1/81/b2/063a67f2b03417d00d9a07be641e28b1f41cd4e9488c35bf3c 2021-07-10T11:35:54,959 Successfully built mdanalysis 2021-07-10T11:35:55,015 Removed build tracker: '/tmp/pip-req-tracker-s6dsc3z7'