2021-07-16T04:22:01,395 Created temporary directory: /tmp/pip-ephem-wheel-cache-n3n2rh0v
2021-07-16T04:22:01,398 Created temporary directory: /tmp/pip-req-tracker-2ufbf6nb
2021-07-16T04:22:01,398 Initialized build tracking at /tmp/pip-req-tracker-2ufbf6nb
2021-07-16T04:22:01,398 Created build tracker: /tmp/pip-req-tracker-2ufbf6nb
2021-07-16T04:22:01,398 Entered build tracker: /tmp/pip-req-tracker-2ufbf6nb
2021-07-16T04:22:01,399 Created temporary directory: /tmp/pip-wheel-9pochtaj
2021-07-16T04:22:01,428 1 location(s) to search for versions of pytim:
2021-07-16T04:22:01,428 * https://pypi.org/simple/pytim/
2021-07-16T04:22:01,429 Fetching project page and analyzing links: https://pypi.org/simple/pytim/
2021-07-16T04:22:01,429 Getting page https://pypi.org/simple/pytim/
2021-07-16T04:22:01,431 Found index url https://pypi.org/simple
2021-07-16T04:22:01,616   Found link https://files.pythonhosted.org/packages/35/4e/a6871590b0fec2bf31b8eafc318bff79ed98fe0eaa44f18254bbadb307dd/pytim-0.5.1.tar.gz#sha256=99dcc3d0860b76bf818fc1e95714369d89bf30c25e692d81e818d3308787d33a (from https://pypi.org/simple/pytim/), version: 0.5.1
2021-07-16T04:22:01,617   Found link https://files.pythonhosted.org/packages/53/3b/840d7adf7edaaf1420f38c01292ab31dd56548d670685805b9b522373501/pytim-0.5.2.tar.gz#sha256=27bf9d793577ea9c0783c4d654ae0d4ad461c9d8da503bd41547287ee3ef0c5b (from https://pypi.org/simple/pytim/), version: 0.5.2
2021-07-16T04:22:01,617   Found link https://files.pythonhosted.org/packages/b8/37/df43d4a2355aae4139a93d77e2d54085d35334fd58a66ec1be69dec025b1/pytim-0.5.3.tar.gz#sha256=e7ae42aa4b4a9707962b245e69800eb562136a696f7b4e14f52d998bca7af7f7 (from https://pypi.org/simple/pytim/), version: 0.5.3
2021-07-16T04:22:01,617   Found link https://files.pythonhosted.org/packages/c2/2a/b3ef26f96069762410993ddc4ac5bb640733810d6e9f6a1b1e74357e8d57/pytim-0.5.4.tar.gz#sha256=9c4938e8f5e00a91bba5264d97b71eab77b48e4b017262a30d1d5533476e2dff (from https://pypi.org/simple/pytim/), version: 0.5.4
2021-07-16T04:22:01,617   Found link https://files.pythonhosted.org/packages/92/49/95e9c00e35b561cc63a1ea5bde8f1c9947dc95c89ce4fc300cffcaa1bf64/pytim-0.5.6.tar.gz#sha256=50c021e3998a6681d0c0c421ebcfabb2d4e823632c32639d4708ffc0774a5145 (from https://pypi.org/simple/pytim/), version: 0.5.6
2021-07-16T04:22:01,618   Found link https://files.pythonhosted.org/packages/d7/a1/6326835075e682ee8aeee36eca3502870fca8df0af93e353852a023e4561/pytim-0.5.7.tar.gz#sha256=ef2ce00d0cf06edec4cf536cf212bc76bc89cbe5d0bf319ac73f0b3f81f4795c (from https://pypi.org/simple/pytim/), version: 0.5.7
2021-07-16T04:22:01,618   Found link https://files.pythonhosted.org/packages/c0/e4/94b9aea18f3cfaa4d3ede623f7655285a07a9d5bce1b4730c1c11bc504a4/pytim-0.6.0.tar.gz#sha256=2b1c0ec37f74733f2369c5eb5087e0fe198cb426fa0ac13a169f0bf810544d83 (from https://pypi.org/simple/pytim/), version: 0.6.0
2021-07-16T04:22:01,618   Found link https://files.pythonhosted.org/packages/1d/51/bf594c173f3a7361be6ceb6838ba751fbac173a3838fa47c6356ccc91a5e/pytim-0.6.1.tar.gz#sha256=7ca2c7ed9c37758a55480779d11bff1184fa715f66c5437181475845423b90f5 (from https://pypi.org/simple/pytim/), version: 0.6.1
2021-07-16T04:22:01,619   Found link https://files.pythonhosted.org/packages/ff/5c/2d4b70fe71a2200f06d517ebe2b6a9600f22346ef74855fe3cf51240dd39/pytim-0.6.2.tar.gz#sha256=fe75c8c31f04e3ebbf416b90fc5dd3b71d537855e674974aa86cb50c8a54ff56 (from https://pypi.org/simple/pytim/), version: 0.6.2
2021-07-16T04:22:01,619   Found link https://files.pythonhosted.org/packages/da/7d/f8fa6f1c50e421e926adcff5f97f0b36e40f6c7dd14dd6005248de6db86e/pytim-0.6.3.tar.gz#sha256=e0d2f20d90c679e6bc8a4e397b2a030d73f4254ec874c017091b55b06532727a (from https://pypi.org/simple/pytim/), version: 0.6.3
2021-07-16T04:22:01,619   Found link https://files.pythonhosted.org/packages/e0/b8/b32af8aacd0a1b96e92accffa4a644e983f978cacc31e45037619246e763/pytim-0.8.0.tar.gz#sha256=d5a65559becebb30fb1ae7b3b769a10cffa484539c2fb246f8f25271b66dc7eb (from https://pypi.org/simple/pytim/), version: 0.8.0
2021-07-16T04:22:01,619   Found link https://files.pythonhosted.org/packages/75/db/20972c9a09acc3ae93ef94e82689bab9e63c6117faa80d25520855694cd8/pytim-0.8.1.tar.gz#sha256=93e934beaead8161404579311d547f7d0320ed21d3f54433f75e69b140c2f7c9 (from https://pypi.org/simple/pytim/), version: 0.8.1
2021-07-16T04:22:01,620   Found link https://files.pythonhosted.org/packages/c9/ab/0524f11f8b570e286011cf6fdd975f06266eb4018d2b10eea2c8a411393f/pytim-0.8.2.tar.gz#sha256=fc816595a92b801e8ad8d6c135758cce6bebc756694b02b561536fe0dbee3879 (from https://pypi.org/simple/pytim/), version: 0.8.2
2021-07-16T04:22:01,620   Found link https://files.pythonhosted.org/packages/9d/56/916297147f61c10aecaf15469c6e128447f2de417f3647ade801e0e882aa/pytim-0.8.3.tar.gz#sha256=4d844caf3ff61dd781ad9e97ffbbb19dd161770a80cf536edb9feaad2fb88394 (from https://pypi.org/simple/pytim/), version: 0.8.3
2021-07-16T04:22:01,620   Found link https://files.pythonhosted.org/packages/9e/5f/3542a5bd383b5148c1f6eda1dbd71e69e96ff7ccc621f8f2e363a3585280/pytim-0.8.4.tar.gz#sha256=bc76da641b4aa1b1264a8b84b331a1db99bb84a705be415d12281e123235b180 (from https://pypi.org/simple/pytim/), version: 0.8.4
2021-07-16T04:22:01,621 Skipping link: not a file: https://pypi.org/simple/pytim/
2021-07-16T04:22:01,641 Given no hashes to check 1 links for project 'pytim': discarding no candidates
2021-07-16T04:22:01,660 Collecting pytim==0.8.2
2021-07-16T04:22:01,661   Created temporary directory: /tmp/pip-unpack-6vwdo_88
2021-07-16T04:22:04,248   Downloading pytim-0.8.2.tar.gz (12.7 MB)
2021-07-16T04:22:06,651   Added pytim==0.8.2 from https://files.pythonhosted.org/packages/c9/ab/0524f11f8b570e286011cf6fdd975f06266eb4018d2b10eea2c8a411393f/pytim-0.8.2.tar.gz#sha256=fc816595a92b801e8ad8d6c135758cce6bebc756694b02b561536fe0dbee3879 to build tracker '/tmp/pip-req-tracker-2ufbf6nb'
2021-07-16T04:22:06,653     Running setup.py (path:/tmp/pip-wheel-9pochtaj/pytim_dd15121c68c5465295ca1357a8b6cb10/setup.py) egg_info for package pytim
2021-07-16T04:22:06,654     Created temporary directory: /tmp/pip-pip-egg-info-5ruet68o
2021-07-16T04:22:06,654     Running command python setup.py egg_info
2021-07-16T04:22:08,401     running egg_info
2021-07-16T04:22:08,403     creating /tmp/pip-pip-egg-info-5ruet68o/pytim.egg-info
2021-07-16T04:22:08,405     writing /tmp/pip-pip-egg-info-5ruet68o/pytim.egg-info/PKG-INFO
2021-07-16T04:22:08,407     writing dependency_links to /tmp/pip-pip-egg-info-5ruet68o/pytim.egg-info/dependency_links.txt
2021-07-16T04:22:08,409     writing requirements to /tmp/pip-pip-egg-info-5ruet68o/pytim.egg-info/requires.txt
2021-07-16T04:22:08,410     writing top-level names to /tmp/pip-pip-egg-info-5ruet68o/pytim.egg-info/top_level.txt
2021-07-16T04:22:08,411     writing manifest file '/tmp/pip-pip-egg-info-5ruet68o/pytim.egg-info/SOURCES.txt'
2021-07-16T04:22:08,624     reading manifest file '/tmp/pip-pip-egg-info-5ruet68o/pytim.egg-info/SOURCES.txt'
2021-07-16T04:22:08,634     writing manifest file '/tmp/pip-pip-egg-info-5ruet68o/pytim.egg-info/SOURCES.txt'
2021-07-16T04:22:08,748   Source in /tmp/pip-wheel-9pochtaj/pytim_dd15121c68c5465295ca1357a8b6cb10 has version 0.8.2, which satisfies requirement pytim==0.8.2 from https://files.pythonhosted.org/packages/c9/ab/0524f11f8b570e286011cf6fdd975f06266eb4018d2b10eea2c8a411393f/pytim-0.8.2.tar.gz#sha256=fc816595a92b801e8ad8d6c135758cce6bebc756694b02b561536fe0dbee3879
2021-07-16T04:22:08,749   Removed pytim==0.8.2 from https://files.pythonhosted.org/packages/c9/ab/0524f11f8b570e286011cf6fdd975f06266eb4018d2b10eea2c8a411393f/pytim-0.8.2.tar.gz#sha256=fc816595a92b801e8ad8d6c135758cce6bebc756694b02b561536fe0dbee3879 from build tracker '/tmp/pip-req-tracker-2ufbf6nb'
2021-07-16T04:22:08,753 Created temporary directory: /tmp/pip-unpack-sgvy9xmr
2021-07-16T04:22:08,753 Building wheels for collected packages: pytim
2021-07-16T04:22:08,757   Created temporary directory: /tmp/pip-wheel-5ljt0d58
2021-07-16T04:22:08,758   Building wheel for pytim (setup.py): started
2021-07-16T04:22:08,758   Destination directory: /tmp/pip-wheel-5ljt0d58
2021-07-16T04:22:08,758   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-9pochtaj/pytim_dd15121c68c5465295ca1357a8b6cb10/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-9pochtaj/pytim_dd15121c68c5465295ca1357a8b6cb10/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-5ljt0d58
2021-07-16T04:22:10,446   running bdist_wheel
2021-07-16T04:22:10,452   running build
2021-07-16T04:22:10,452   running build_py
2021-07-16T04:22:10,589   creating build
2021-07-16T04:22:10,589   creating build/lib.linux-armv7l-3.9
2021-07-16T04:22:10,590   creating build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,591   copying pytim/simple_interface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,594   copying pytim/itim.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,596   copying pytim/properties.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,598   copying pytim/surface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,600   copying pytim/atoms_maps.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,603   copying pytim/gitim.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,605   copying pytim/vtk.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,608   copying pytim/cube.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,610   copying pytim/utilities_mesh.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,612   copying pytim/interface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,614   copying pytim/utilities_geometry.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,617   copying pytim/writepdb.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,619   copying pytim/utilities_dbscan.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,621   copying pytim/sasa.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,624   copying pytim/sanity_check.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,627   copying pytim/messages.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,629   copying pytim/patches.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,631   copying pytim/wavefront_obj.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,633   copying pytim/__init__.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,635   copying pytim/gaussian_kde_pbc.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,637   copying pytim/version.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,638   copying pytim/willard_chandler.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,641   copying pytim/utilities.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,643   copying pytim/utilities_pbc.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,645   copying pytim/chacon_tarazona.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:22:10,648   creating build/lib.linux-armv7l-3.9/pytim/datafiles
2021-07-16T04:22:10,649   copying pytim/datafiles/__init__.py -> build/lib.linux-armv7l-3.9/pytim/datafiles
2021-07-16T04:22:10,653   creating build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,653   copying pytim/observables/rdf.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,656   copying pytim/observables/free_volume.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,658   copying pytim/observables/basic_observables.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,661   copying pytim/observables/distributionfunction.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,663   copying pytim/observables/profile.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,666   copying pytim/observables/rdf2d.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,668   copying pytim/observables/intrinsic_distance.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,670   copying pytim/observables/__init__.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,672   copying pytim/observables/observable.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,675   copying pytim/observables/orientation.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,676   copying pytim/observables/local_frame.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,679   copying pytim/observables/correlator.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,682   copying pytim/observables/layer_triangulation.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:22:10,687   creating build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,688   copying pytim/data/micelle.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,724   copying pytim/data/logo.pdf -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,727   copying pytim/data/ilbenzene.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,817   copying pytim/data/water.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,848   copying pytim/data/ffamber03.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,851   copying pytim/data/water.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,938   copying pytim/data/water_520K.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,945   copying pytim/data/water_550K.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:10,953   copying pytim/data/dppc.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,014   copying pytim/data/water-small.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,017   copying pytim/data/fullerene.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,020   copying pytim/data/glucose.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,024   copying pytim/data/_test_bcc.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,027   copying pytim/data/methanol.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,046   copying pytim/data/ffcharmm27.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,052   copying pytim/data/logo.svg -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,055   copying pytim/data/LJ.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,091   copying pytim/data/water_lmp.data -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,167   copying pytim/data/CCL4.H2O.GRO -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,261   copying pytim/data/water.xyz -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,272   copying pytim/data/ffg43a1.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,278   copying pytim/data/water.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,303   copying pytim/data/_test_profile.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,305   copying pytim/data/LJ.short.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,364   copying pytim/data/water_lmp.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,385   copying pytim/data/_test_orientation.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:22:11,390   running build_ext
2021-07-16T04:22:11,478   cythoning pytim/dbscan_inner.pyx to pytim/dbscan_inner.cpp
2021-07-16T04:22:12,080   /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-9pochtaj/pytim_dd15121c68c5465295ca1357a8b6cb10/pytim/dbscan_inner.pyx
2021-07-16T04:22:12,080     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-16T04:22:13,691   cythoning pytim/circumradius.pyx to pytim/circumradius.cpp
2021-07-16T04:22:13,697   /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-9pochtaj/pytim_dd15121c68c5465295ca1357a8b6cb10/pytim/circumradius.pyx
2021-07-16T04:22:13,697     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-16T04:22:28,097   building 'pytim_dbscan' extension
2021-07-16T04:22:28,097   creating build/temp.linux-armv7l-3.9
2021-07-16T04:22:28,097   creating build/temp.linux-armv7l-3.9/pytim
2021-07-16T04:22:28,098   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c pytim/dbscan_inner.cpp -o build/temp.linux-armv7l-3.9/pytim/dbscan_inner.o
2021-07-16T04:22:28,545   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T04:22:28,545                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T04:22:28,545                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T04:22:28,545                    from pytim/dbscan_inner.cpp:644:
2021-07-16T04:22:28,546   /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-16T04:22:28,546      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T04:22:28,546         |  ^~~~~~~
2021-07-16T04:22:32,150   arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pytim/dbscan_inner.o -o build/lib.linux-armv7l-3.9/pytim_dbscan.cpython-39-arm-linux-gnueabihf.so
2021-07-16T04:22:32,430   building 'circumradius' extension
2021-07-16T04:22:32,430   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c pytim/circumradius.cpp -o build/temp.linux-armv7l-3.9/pytim/circumradius.o
2021-07-16T04:22:32,858   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T04:22:32,859                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T04:22:32,859                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T04:22:32,859                    from pytim/circumradius.cpp:627:
2021-07-16T04:22:32,859   /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-16T04:22:32,859      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T04:22:32,859         |  ^~~~~~~
2021-07-16T04:22:34,000   pytim/circumradius.cpp: In function ‘PyObject* __pyx_f_12circumradius__circumradius(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’:
2021-07-16T04:22:34,000   pytim/circumradius.cpp:2754:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2021-07-16T04:22:34,001    2754 |   for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
2021-07-16T04:22:34,001         |                       ~~~~~~~~~~^~~~~~~~~~~
2021-07-16T04:22:45,521   arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/pytim/circumradius.o -o build/lib.linux-armv7l-3.9/circumradius.cpython-39-arm-linux-gnueabihf.so
2021-07-16T04:22:45,751   installing to build/bdist.linux-armv7l/wheel
2021-07-16T04:22:45,751   running install
2021-07-16T04:22:45,753   running install_lib
2021-07-16T04:22:45,757   creating build/bdist.linux-armv7l
2021-07-16T04:22:45,757   creating build/bdist.linux-armv7l/wheel
2021-07-16T04:22:45,759   creating build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,761   creating build/bdist.linux-armv7l/wheel/pytim/datafiles
2021-07-16T04:22:45,762   copying build/lib.linux-armv7l-3.9/pytim/datafiles/__init__.py -> build/bdist.linux-armv7l/wheel/pytim/datafiles
2021-07-16T04:22:45,765   copying build/lib.linux-armv7l-3.9/pytim/simple_interface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,767   copying build/lib.linux-armv7l-3.9/pytim/itim.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,770   creating build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,771   copying build/lib.linux-armv7l-3.9/pytim/observables/rdf.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,773   copying build/lib.linux-armv7l-3.9/pytim/observables/free_volume.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,776   copying build/lib.linux-armv7l-3.9/pytim/observables/basic_observables.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,778   copying build/lib.linux-armv7l-3.9/pytim/observables/distributionfunction.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,781   copying build/lib.linux-armv7l-3.9/pytim/observables/profile.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,784   copying build/lib.linux-armv7l-3.9/pytim/observables/rdf2d.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,786   copying build/lib.linux-armv7l-3.9/pytim/observables/intrinsic_distance.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,788   copying build/lib.linux-armv7l-3.9/pytim/observables/__init__.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,790   copying build/lib.linux-armv7l-3.9/pytim/observables/observable.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,792   copying build/lib.linux-armv7l-3.9/pytim/observables/orientation.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,794   copying build/lib.linux-armv7l-3.9/pytim/observables/local_frame.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,796   copying build/lib.linux-armv7l-3.9/pytim/observables/correlator.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,799   copying build/lib.linux-armv7l-3.9/pytim/observables/layer_triangulation.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:22:45,801   copying build/lib.linux-armv7l-3.9/pytim/properties.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,804   copying build/lib.linux-armv7l-3.9/pytim/surface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,806   copying build/lib.linux-armv7l-3.9/pytim/atoms_maps.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,809   copying build/lib.linux-armv7l-3.9/pytim/gitim.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,812   copying build/lib.linux-armv7l-3.9/pytim/vtk.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,814   copying build/lib.linux-armv7l-3.9/pytim/cube.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,816   copying build/lib.linux-armv7l-3.9/pytim/utilities_mesh.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:45,819   creating build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:45,820   copying build/lib.linux-armv7l-3.9/pytim/data/micelle.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:45,854   copying build/lib.linux-armv7l-3.9/pytim/data/logo.pdf -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:45,856   copying build/lib.linux-armv7l-3.9/pytim/data/ilbenzene.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:45,931   copying build/lib.linux-armv7l-3.9/pytim/data/water.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:45,954   copying build/lib.linux-armv7l-3.9/pytim/data/ffamber03.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:45,957   copying build/lib.linux-armv7l-3.9/pytim/data/water.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,047   copying build/lib.linux-armv7l-3.9/pytim/data/water_520K.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,057   copying build/lib.linux-armv7l-3.9/pytim/data/water_550K.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,064   copying build/lib.linux-armv7l-3.9/pytim/data/dppc.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,123   copying build/lib.linux-armv7l-3.9/pytim/data/water-small.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,127   copying build/lib.linux-armv7l-3.9/pytim/data/fullerene.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,129   copying build/lib.linux-armv7l-3.9/pytim/data/glucose.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,133   copying build/lib.linux-armv7l-3.9/pytim/data/_test_bcc.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,135   copying build/lib.linux-armv7l-3.9/pytim/data/methanol.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,164   copying build/lib.linux-armv7l-3.9/pytim/data/ffcharmm27.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,169   copying build/lib.linux-armv7l-3.9/pytim/data/logo.svg -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,170   copying build/lib.linux-armv7l-3.9/pytim/data/LJ.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,202   copying build/lib.linux-armv7l-3.9/pytim/data/water_lmp.data -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,227   copying build/lib.linux-armv7l-3.9/pytim/data/CCL4.H2O.GRO -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,300   copying build/lib.linux-armv7l-3.9/pytim/data/water.xyz -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,307   copying build/lib.linux-armv7l-3.9/pytim/data/ffg43a1.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,312   copying build/lib.linux-armv7l-3.9/pytim/data/water.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,341   copying build/lib.linux-armv7l-3.9/pytim/data/_test_profile.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,343   copying build/lib.linux-armv7l-3.9/pytim/data/LJ.short.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,411   copying build/lib.linux-armv7l-3.9/pytim/data/water_lmp.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,426   copying build/lib.linux-armv7l-3.9/pytim/data/_test_orientation.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:22:46,429   copying build/lib.linux-armv7l-3.9/pytim/interface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,432   copying build/lib.linux-armv7l-3.9/pytim/utilities_geometry.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,435   copying build/lib.linux-armv7l-3.9/pytim/writepdb.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,438   copying build/lib.linux-armv7l-3.9/pytim/utilities_dbscan.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,440   copying build/lib.linux-armv7l-3.9/pytim/sasa.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,443   copying build/lib.linux-armv7l-3.9/pytim/sanity_check.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,446   copying build/lib.linux-armv7l-3.9/pytim/messages.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,448   copying build/lib.linux-armv7l-3.9/pytim/patches.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,450   copying build/lib.linux-armv7l-3.9/pytim/wavefront_obj.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,452   copying build/lib.linux-armv7l-3.9/pytim/__init__.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,454   copying build/lib.linux-armv7l-3.9/pytim/gaussian_kde_pbc.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,457   copying build/lib.linux-armv7l-3.9/pytim/version.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,459   copying build/lib.linux-armv7l-3.9/pytim/willard_chandler.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,462   copying build/lib.linux-armv7l-3.9/pytim/utilities.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,465   copying build/lib.linux-armv7l-3.9/pytim/utilities_pbc.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,468   copying build/lib.linux-armv7l-3.9/pytim/chacon_tarazona.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:22:46,471   copying build/lib.linux-armv7l-3.9/circumradius.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2021-07-16T04:22:46,494   copying build/lib.linux-armv7l-3.9/pytim_dbscan.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2021-07-16T04:22:46,503   running install_egg_info
2021-07-16T04:22:46,526   running egg_info
2021-07-16T04:22:46,527   writing pytim.egg-info/PKG-INFO
2021-07-16T04:22:46,529   writing dependency_links to pytim.egg-info/dependency_links.txt
2021-07-16T04:22:46,531   writing requirements to pytim.egg-info/requires.txt
2021-07-16T04:22:46,532   writing top-level names to pytim.egg-info/top_level.txt
2021-07-16T04:22:46,584   reading manifest file 'pytim.egg-info/SOURCES.txt'
2021-07-16T04:22:46,597   writing manifest file 'pytim.egg-info/SOURCES.txt'
2021-07-16T04:22:46,599   Copying pytim.egg-info to build/bdist.linux-armv7l/wheel/pytim-0.8.2-py3.9.egg-info
2021-07-16T04:22:46,610   running install_scripts
2021-07-16T04:22:46,674   creating build/bdist.linux-armv7l/wheel/pytim-0.8.2.dist-info/WHEEL
2021-07-16T04:22:46,676   creating '/tmp/pip-wheel-5ljt0d58/pytim-0.8.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-16T04:22:46,852   adding 'circumradius.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T04:22:46,907   adding 'pytim_dbscan.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T04:22:46,912   adding 'pytim/__init__.py'
2021-07-16T04:22:46,913   adding 'pytim/atoms_maps.py'
2021-07-16T04:22:46,915   adding 'pytim/chacon_tarazona.py'
2021-07-16T04:22:46,916   adding 'pytim/cube.py'
2021-07-16T04:22:46,918   adding 'pytim/gaussian_kde_pbc.py'
2021-07-16T04:22:46,920   adding 'pytim/gitim.py'
2021-07-16T04:22:46,923   adding 'pytim/interface.py'
2021-07-16T04:22:46,926   adding 'pytim/itim.py'
2021-07-16T04:22:46,927   adding 'pytim/messages.py'
2021-07-16T04:22:46,929   adding 'pytim/patches.py'
2021-07-16T04:22:46,930   adding 'pytim/properties.py'
2021-07-16T04:22:46,932   adding 'pytim/sanity_check.py'
2021-07-16T04:22:46,934   adding 'pytim/sasa.py'
2021-07-16T04:22:46,936   adding 'pytim/simple_interface.py'
2021-07-16T04:22:46,938   adding 'pytim/surface.py'
2021-07-16T04:22:46,940   adding 'pytim/utilities.py'
2021-07-16T04:22:46,941   adding 'pytim/utilities_dbscan.py'
2021-07-16T04:22:46,943   adding 'pytim/utilities_geometry.py'
2021-07-16T04:22:46,944   adding 'pytim/utilities_mesh.py'
2021-07-16T04:22:46,946   adding 'pytim/utilities_pbc.py'
2021-07-16T04:22:46,947   adding 'pytim/version.py'
2021-07-16T04:22:46,948   adding 'pytim/vtk.py'
2021-07-16T04:22:46,950   adding 'pytim/wavefront_obj.py'
2021-07-16T04:22:46,951   adding 'pytim/willard_chandler.py'
2021-07-16T04:22:46,953   adding 'pytim/writepdb.py'
2021-07-16T04:22:47,914   adding 'pytim/data/CCL4.H2O.GRO'
2021-07-16T04:22:48,308   adding 'pytim/data/LJ.gro'
2021-07-16T04:22:48,607   adding 'pytim/data/LJ.short.xtc'
2021-07-16T04:22:48,629   adding 'pytim/data/_test_bcc.gro'
2021-07-16T04:22:48,630   adding 'pytim/data/_test_orientation.gro'
2021-07-16T04:22:48,631   adding 'pytim/data/_test_profile.gro'
2021-07-16T04:22:49,380   adding 'pytim/data/dppc.gro'
2021-07-16T04:22:49,402   adding 'pytim/data/ffamber03.nonbonded.itp'
2021-07-16T04:22:49,410   adding 'pytim/data/ffcharmm27.nonbonded.itp'
2021-07-16T04:22:49,422   adding 'pytim/data/ffg43a1.nonbonded.itp'
2021-07-16T04:22:49,424   adding 'pytim/data/fullerene.pdb'
2021-07-16T04:22:49,430   adding 'pytim/data/glucose.pdb'
2021-07-16T04:22:50,435   adding 'pytim/data/ilbenzene.gro'
2021-07-16T04:22:50,464   adding 'pytim/data/logo.pdf'
2021-07-16T04:22:50,466   adding 'pytim/data/logo.svg'
2021-07-16T04:22:50,703   adding 'pytim/data/methanol.gro'
2021-07-16T04:22:50,907   adding 'pytim/data/micelle.pdb'
2021-07-16T04:22:50,925   adding 'pytim/data/water-small.gro'
2021-07-16T04:22:51,169   adding 'pytim/data/water.gro'
2021-07-16T04:22:51,291   adding 'pytim/data/water.pdb'
2021-07-16T04:22:51,784   adding 'pytim/data/water.xtc'
2021-07-16T04:22:51,908   adding 'pytim/data/water.xyz'
2021-07-16T04:22:51,970   adding 'pytim/data/water_520K.gro'
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2021-07-16T04:22:52,279   adding 'pytim/data/water_lmp.data'
2021-07-16T04:22:52,354   adding 'pytim/data/water_lmp.xtc'
2021-07-16T04:22:52,361   adding 'pytim/datafiles/__init__.py'
2021-07-16T04:22:52,364   adding 'pytim/observables/__init__.py'
2021-07-16T04:22:52,365   adding 'pytim/observables/basic_observables.py'
2021-07-16T04:22:52,368   adding 'pytim/observables/correlator.py'
2021-07-16T04:22:52,370   adding 'pytim/observables/distributionfunction.py'
2021-07-16T04:22:52,371   adding 'pytim/observables/free_volume.py'
2021-07-16T04:22:52,373   adding 'pytim/observables/intrinsic_distance.py'
2021-07-16T04:22:52,374   adding 'pytim/observables/layer_triangulation.py'
2021-07-16T04:22:52,376   adding 'pytim/observables/local_frame.py'
2021-07-16T04:22:52,377   adding 'pytim/observables/observable.py'
2021-07-16T04:22:52,379   adding 'pytim/observables/orientation.py'
2021-07-16T04:22:52,381   adding 'pytim/observables/profile.py'
2021-07-16T04:22:52,383   adding 'pytim/observables/rdf.py'
2021-07-16T04:22:52,384   adding 'pytim/observables/rdf2d.py'
2021-07-16T04:22:52,386   adding 'pytim-0.8.2.dist-info/METADATA'
2021-07-16T04:22:52,387   adding 'pytim-0.8.2.dist-info/WHEEL'
2021-07-16T04:22:52,394   adding 'pytim-0.8.2.dist-info/top_level.txt'
2021-07-16T04:22:52,396   adding 'pytim-0.8.2.dist-info/RECORD'
2021-07-16T04:22:52,574   removing build/bdist.linux-armv7l/wheel
2021-07-16T04:22:53,211   Building wheel for pytim (setup.py): finished with status 'done'
2021-07-16T04:22:53,379   Created wheel for pytim: filename=pytim-0.8.2-cp39-cp39-linux_armv7l.whl size=13212174 sha256=2b2ef618ab580147dd05f4febdf2e003934416e8239ad4df8211ad21d0d5c7ea
2021-07-16T04:22:53,380   Stored in directory: /tmp/pip-ephem-wheel-cache-n3n2rh0v/wheels/01/9a/63/b7844a1abe91d4d67f4718d8a5d127fd1d75647e22329ec46b
2021-07-16T04:22:53,397 Successfully built pytim
2021-07-16T04:22:53,755 Removed build tracker: '/tmp/pip-req-tracker-2ufbf6nb'