2021-07-16T11:09:59,346 Created temporary directory: /tmp/pip-ephem-wheel-cache-7u49rbsy
2021-07-16T11:09:59,349 Created temporary directory: /tmp/pip-req-tracker-64rzzmzj
2021-07-16T11:09:59,349 Initialized build tracking at /tmp/pip-req-tracker-64rzzmzj
2021-07-16T11:09:59,349 Created build tracker: /tmp/pip-req-tracker-64rzzmzj
2021-07-16T11:09:59,349 Entered build tracker: /tmp/pip-req-tracker-64rzzmzj
2021-07-16T11:09:59,350 Created temporary directory: /tmp/pip-wheel-yo4wmu0d
2021-07-16T11:09:59,379 1 location(s) to search for versions of pytim:
2021-07-16T11:09:59,379 * https://pypi.org/simple/pytim/
2021-07-16T11:09:59,379 Fetching project page and analyzing links: https://pypi.org/simple/pytim/
2021-07-16T11:09:59,380 Getting page https://pypi.org/simple/pytim/
2021-07-16T11:09:59,381 Found index url https://pypi.org/simple
2021-07-16T11:09:59,566   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
2021-07-16T11:09:59,566   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
2021-07-16T11:09:59,567   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
2021-07-16T11:09:59,567   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
2021-07-16T11:09:59,567   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
2021-07-16T11:09:59,568   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
2021-07-16T11:09:59,568   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
2021-07-16T11:09:59,568   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
2021-07-16T11:09:59,569   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
2021-07-16T11:09:59,569   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
2021-07-16T11:09:59,569   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
2021-07-16T11:09:59,570   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
2021-07-16T11:09:59,570   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
2021-07-16T11:09:59,570   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
2021-07-16T11:09:59,570   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
2021-07-16T11:09:59,571 Skipping link: not a file: https://pypi.org/simple/pytim/
2021-07-16T11:09:59,590 Given no hashes to check 1 links for project 'pytim': discarding no candidates
2021-07-16T11:09:59,609 Collecting pytim==0.8.4
2021-07-16T11:09:59,610   Created temporary directory: /tmp/pip-unpack-reinsl4v
2021-07-16T11:10:00,357   Downloading pytim-0.8.4.tar.gz (13.6 MB)
2021-07-16T11:10:02,766   Added pytim==0.8.4 from https://files.pythonhosted.org/packages/9e/5f/3542a5bd383b5148c1f6eda1dbd71e69e96ff7ccc621f8f2e363a3585280/pytim-0.8.4.tar.gz#sha256=bc76da641b4aa1b1264a8b84b331a1db99bb84a705be415d12281e123235b180 to build tracker '/tmp/pip-req-tracker-64rzzmzj'
2021-07-16T11:10:02,767     Running setup.py (path:/tmp/pip-wheel-yo4wmu0d/pytim_dc898880cd9243e185c463de861d442d/setup.py) egg_info for package pytim
2021-07-16T11:10:02,768     Created temporary directory: /tmp/pip-pip-egg-info-xr2sdtyd
2021-07-16T11:10:02,768     Running command python setup.py egg_info
2021-07-16T11:10:04,581     running egg_info
2021-07-16T11:10:04,583     creating /tmp/pip-pip-egg-info-xr2sdtyd/pytim.egg-info
2021-07-16T11:10:04,585     writing /tmp/pip-pip-egg-info-xr2sdtyd/pytim.egg-info/PKG-INFO
2021-07-16T11:10:04,587     writing dependency_links to /tmp/pip-pip-egg-info-xr2sdtyd/pytim.egg-info/dependency_links.txt
2021-07-16T11:10:04,588     writing requirements to /tmp/pip-pip-egg-info-xr2sdtyd/pytim.egg-info/requires.txt
2021-07-16T11:10:04,589     writing top-level names to /tmp/pip-pip-egg-info-xr2sdtyd/pytim.egg-info/top_level.txt
2021-07-16T11:10:04,591     writing manifest file '/tmp/pip-pip-egg-info-xr2sdtyd/pytim.egg-info/SOURCES.txt'
2021-07-16T11:10:04,778     reading manifest file '/tmp/pip-pip-egg-info-xr2sdtyd/pytim.egg-info/SOURCES.txt'
2021-07-16T11:10:04,786     writing manifest file '/tmp/pip-pip-egg-info-xr2sdtyd/pytim.egg-info/SOURCES.txt'
2021-07-16T11:10:04,902   Source in /tmp/pip-wheel-yo4wmu0d/pytim_dc898880cd9243e185c463de861d442d has version 0.8.4, which satisfies requirement pytim==0.8.4 from https://files.pythonhosted.org/packages/9e/5f/3542a5bd383b5148c1f6eda1dbd71e69e96ff7ccc621f8f2e363a3585280/pytim-0.8.4.tar.gz#sha256=bc76da641b4aa1b1264a8b84b331a1db99bb84a705be415d12281e123235b180
2021-07-16T11:10:04,903   Removed pytim==0.8.4 from https://files.pythonhosted.org/packages/9e/5f/3542a5bd383b5148c1f6eda1dbd71e69e96ff7ccc621f8f2e363a3585280/pytim-0.8.4.tar.gz#sha256=bc76da641b4aa1b1264a8b84b331a1db99bb84a705be415d12281e123235b180 from build tracker '/tmp/pip-req-tracker-64rzzmzj'
2021-07-16T11:10:04,907 Created temporary directory: /tmp/pip-unpack-04ed4cqo
2021-07-16T11:10:04,907 Building wheels for collected packages: pytim
2021-07-16T11:10:04,913   Created temporary directory: /tmp/pip-wheel-glejytmf
2021-07-16T11:10:04,914   Building wheel for pytim (setup.py): started
2021-07-16T11:10:04,914   Destination directory: /tmp/pip-wheel-glejytmf
2021-07-16T11:10:04,914   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-yo4wmu0d/pytim_dc898880cd9243e185c463de861d442d/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-yo4wmu0d/pytim_dc898880cd9243e185c463de861d442d/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-glejytmf
2021-07-16T11:10:07,003   running bdist_wheel
2021-07-16T11:10:07,008   running build
2021-07-16T11:10:07,009   running build_py
2021-07-16T11:10:07,146   creating build
2021-07-16T11:10:07,147   creating build/lib.linux-armv7l-3.9
2021-07-16T11:10:07,148   creating build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,149   copying pytim/chacon_tarazona.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,152   copying pytim/messages.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,155   copying pytim/__init__.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,156   copying pytim/writepdb.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,159   copying pytim/interface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,162   copying pytim/utilities_dbscan.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,164   copying pytim/utilities_geometry.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,166   copying pytim/wavefront_obj.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,168   copying pytim/atoms_maps.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,170   copying pytim/surface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,173   copying pytim/utilities.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,175   copying pytim/vtk.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,178   copying pytim/willard_chandler.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,181   copying pytim/utilities_pbc.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,183   copying pytim/itim.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,186   copying pytim/gaussian_kde_pbc.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,188   copying pytim/utilities_mesh.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,190   copying pytim/sanity_check.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,193   copying pytim/simple_interface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,195   copying pytim/properties.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,197   copying pytim/sasa.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,200   copying pytim/cube.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,202   copying pytim/patches.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,204   copying pytim/gitim.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,207   copying pytim/version.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T11:10:07,210   creating build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,211   copying pytim/observables/layer_triangulation.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,213   copying pytim/observables/distributionfunction.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,216   copying pytim/observables/__init__.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,217   copying pytim/observables/profile.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,220   copying pytim/observables/correlator.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,226   copying pytim/observables/rdf.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,229   copying pytim/observables/rdf2d.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,232   copying pytim/observables/basic_observables.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,235   copying pytim/observables/free_volume.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,238   copying pytim/observables/local_frame.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,241   copying pytim/observables/intrinsic_distance.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,244   copying pytim/observables/observable.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,248   copying pytim/observables/orientation.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T11:10:07,252   creating build/lib.linux-armv7l-3.9/pytim/datafiles
2021-07-16T11:10:07,253   copying pytim/datafiles/__init__.py -> build/lib.linux-armv7l-3.9/pytim/datafiles
2021-07-16T11:10:07,259   creating build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,260   copying pytim/data/CCL4.H2O.GRO -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,328   copying pytim/data/_test_orientation.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,331   copying pytim/data/water_lmp.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,359   copying pytim/data/ilbenzene.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,437   copying pytim/data/water.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,459   copying pytim/data/water.xyz -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,471   copying pytim/data/LJ.short.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,531   copying pytim/data/water.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,619   copying pytim/data/fullerene.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,621   copying pytim/data/_test_profile.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,623   copying pytim/data/ffg43a1.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,629   copying pytim/data/glucose.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,633   copying pytim/data/ffamber03.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,636   copying pytim/data/water.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,660   copying pytim/data/water-small.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,663   copying pytim/data/water_lmp.data -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,687   copying pytim/data/logo.pdf -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,689   copying pytim/data/water_520K.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,697   copying pytim/data/micelle.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,730   copying pytim/data/logo.svg -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,733   copying pytim/data/dppc.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,789   copying pytim/data/_test_bcc.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,792   copying pytim/data/LJ.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,829   copying pytim/data/methanol.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,852   copying pytim/data/ffcharmm27.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,857   copying pytim/data/antagonistic.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,924   copying pytim/data/water_550K.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T11:10:07,934   running build_ext
2021-07-16T11:10:08,026   cythoning pytim/dbscan_inner.pyx to pytim/dbscan_inner.cpp
2021-07-16T11:10:08,635   /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-yo4wmu0d/pytim_dc898880cd9243e185c463de861d442d/pytim/dbscan_inner.pyx
2021-07-16T11:10:08,635     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-16T11:10:10,198   cythoning pytim/circumradius.pyx to pytim/circumradius.cpp
2021-07-16T11:10:10,204   /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-yo4wmu0d/pytim_dc898880cd9243e185c463de861d442d/pytim/circumradius.pyx
2021-07-16T11:10:10,205     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-16T11:10:24,497   building 'pytim_dbscan' extension
2021-07-16T11:10:24,498   creating build/temp.linux-armv7l-3.9
2021-07-16T11:10:24,498   creating build/temp.linux-armv7l-3.9/pytim
2021-07-16T11:10:24,499   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
2021-07-16T11:10:24,959   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T11:10:24,960                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T11:10:24,960                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T11:10:24,960                    from pytim/dbscan_inner.cpp:644:
2021-07-16T11:10:24,960   /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]
2021-07-16T11:10:24,960      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T11:10:24,961         |  ^~~~~~~
2021-07-16T11:10:28,560   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
2021-07-16T11:10:28,841   building 'circumradius' extension
2021-07-16T11:10:28,842   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
2021-07-16T11:10:29,133   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T11:10:29,134                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T11:10:29,134                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T11:10:29,134                    from pytim/circumradius.cpp:627:
2021-07-16T11:10:29,134   /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]
2021-07-16T11:10:29,135      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T11:10:29,135         |  ^~~~~~~
2021-07-16T11:10:30,272   pytim/circumradius.cpp: In function ‘PyObject* __pyx_f_12circumradius__circumradius(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’:
2021-07-16T11:10:30,273   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]
2021-07-16T11:10:30,273    2754 |   for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
2021-07-16T11:10:30,273         |                       ~~~~~~~~~~^~~~~~~~~~~
2021-07-16T11:10:41,801   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
2021-07-16T11:10:42,037   installing to build/bdist.linux-armv7l/wheel
2021-07-16T11:10:42,037   running install
2021-07-16T11:10:42,038   running install_lib
2021-07-16T11:10:42,043   creating build/bdist.linux-armv7l
2021-07-16T11:10:42,044   creating build/bdist.linux-armv7l/wheel
2021-07-16T11:10:42,045   copying build/lib.linux-armv7l-3.9/pytim_dbscan.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2021-07-16T11:10:42,054   creating build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,056   creating build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,057   copying build/lib.linux-armv7l-3.9/pytim/observables/layer_triangulation.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,059   copying build/lib.linux-armv7l-3.9/pytim/observables/distributionfunction.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,062   copying build/lib.linux-armv7l-3.9/pytim/observables/__init__.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,064   copying build/lib.linux-armv7l-3.9/pytim/observables/profile.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,067   copying build/lib.linux-armv7l-3.9/pytim/observables/correlator.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,069   copying build/lib.linux-armv7l-3.9/pytim/observables/rdf.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,072   copying build/lib.linux-armv7l-3.9/pytim/observables/rdf2d.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,075   copying build/lib.linux-armv7l-3.9/pytim/observables/basic_observables.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,078   copying build/lib.linux-armv7l-3.9/pytim/observables/free_volume.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,081   copying build/lib.linux-armv7l-3.9/pytim/observables/local_frame.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,083   copying build/lib.linux-armv7l-3.9/pytim/observables/intrinsic_distance.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,085   copying build/lib.linux-armv7l-3.9/pytim/observables/observable.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,088   copying build/lib.linux-armv7l-3.9/pytim/observables/orientation.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T11:10:42,091   copying build/lib.linux-armv7l-3.9/pytim/chacon_tarazona.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,094   copying build/lib.linux-armv7l-3.9/pytim/messages.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,096   copying build/lib.linux-armv7l-3.9/pytim/__init__.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,098   copying build/lib.linux-armv7l-3.9/pytim/writepdb.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,101   copying build/lib.linux-armv7l-3.9/pytim/interface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,104   copying build/lib.linux-armv7l-3.9/pytim/utilities_dbscan.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,107   copying build/lib.linux-armv7l-3.9/pytim/utilities_geometry.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,109   copying build/lib.linux-armv7l-3.9/pytim/wavefront_obj.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,112   copying build/lib.linux-armv7l-3.9/pytim/atoms_maps.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,115   creating build/bdist.linux-armv7l/wheel/pytim/datafiles
2021-07-16T11:10:42,116   copying build/lib.linux-armv7l-3.9/pytim/datafiles/__init__.py -> build/bdist.linux-armv7l/wheel/pytim/datafiles
2021-07-16T11:10:42,119   copying build/lib.linux-armv7l-3.9/pytim/surface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,122   copying build/lib.linux-armv7l-3.9/pytim/utilities.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,125   copying build/lib.linux-armv7l-3.9/pytim/vtk.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,127   copying build/lib.linux-armv7l-3.9/pytim/willard_chandler.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,130   copying build/lib.linux-armv7l-3.9/pytim/utilities_pbc.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,133   copying build/lib.linux-armv7l-3.9/pytim/itim.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,135   copying build/lib.linux-armv7l-3.9/pytim/gaussian_kde_pbc.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,138   copying build/lib.linux-armv7l-3.9/pytim/utilities_mesh.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,140   copying build/lib.linux-armv7l-3.9/pytim/sanity_check.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,143   copying build/lib.linux-armv7l-3.9/pytim/simple_interface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,146   copying build/lib.linux-armv7l-3.9/pytim/properties.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,149   copying build/lib.linux-armv7l-3.9/pytim/sasa.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,152   copying build/lib.linux-armv7l-3.9/pytim/cube.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,154   copying build/lib.linux-armv7l-3.9/pytim/patches.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,157   copying build/lib.linux-armv7l-3.9/pytim/gitim.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,161   creating build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,162   copying build/lib.linux-armv7l-3.9/pytim/data/CCL4.H2O.GRO -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,233   copying build/lib.linux-armv7l-3.9/pytim/data/_test_orientation.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,234   copying build/lib.linux-armv7l-3.9/pytim/data/water_lmp.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,251   copying build/lib.linux-armv7l-3.9/pytim/data/ilbenzene.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,333   copying build/lib.linux-armv7l-3.9/pytim/data/water.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,353   copying build/lib.linux-armv7l-3.9/pytim/data/water.xyz -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,361   copying build/lib.linux-armv7l-3.9/pytim/data/LJ.short.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,423   copying build/lib.linux-armv7l-3.9/pytim/data/water.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,519   copying build/lib.linux-armv7l-3.9/pytim/data/fullerene.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,522   copying build/lib.linux-armv7l-3.9/pytim/data/_test_profile.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,523   copying build/lib.linux-armv7l-3.9/pytim/data/ffg43a1.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,528   copying build/lib.linux-armv7l-3.9/pytim/data/glucose.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,531   copying build/lib.linux-armv7l-3.9/pytim/data/ffamber03.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,533   copying build/lib.linux-armv7l-3.9/pytim/data/water.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,560   copying build/lib.linux-armv7l-3.9/pytim/data/water-small.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,563   copying build/lib.linux-armv7l-3.9/pytim/data/water_lmp.data -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,587   copying build/lib.linux-armv7l-3.9/pytim/data/logo.pdf -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,589   copying build/lib.linux-armv7l-3.9/pytim/data/water_520K.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,598   copying build/lib.linux-armv7l-3.9/pytim/data/micelle.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,635   copying build/lib.linux-armv7l-3.9/pytim/data/logo.svg -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,638   copying build/lib.linux-armv7l-3.9/pytim/data/dppc.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,693   copying build/lib.linux-armv7l-3.9/pytim/data/_test_bcc.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,696   copying build/lib.linux-armv7l-3.9/pytim/data/LJ.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,731   copying build/lib.linux-armv7l-3.9/pytim/data/methanol.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,754   copying build/lib.linux-armv7l-3.9/pytim/data/ffcharmm27.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,758   copying build/lib.linux-armv7l-3.9/pytim/data/antagonistic.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,824   copying build/lib.linux-armv7l-3.9/pytim/data/water_550K.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T11:10:42,831   copying build/lib.linux-armv7l-3.9/pytim/version.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T11:10:42,833   copying build/lib.linux-armv7l-3.9/circumradius.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2021-07-16T11:10:42,854   running install_egg_info
2021-07-16T11:10:42,879   running egg_info
2021-07-16T11:10:42,881   writing pytim.egg-info/PKG-INFO
2021-07-16T11:10:42,883   writing dependency_links to pytim.egg-info/dependency_links.txt
2021-07-16T11:10:42,885   writing requirements to pytim.egg-info/requires.txt
2021-07-16T11:10:42,887   writing top-level names to pytim.egg-info/top_level.txt
2021-07-16T11:10:42,942   reading manifest file 'pytim.egg-info/SOURCES.txt'
2021-07-16T11:10:42,954   writing manifest file 'pytim.egg-info/SOURCES.txt'
2021-07-16T11:10:42,957   Copying pytim.egg-info to build/bdist.linux-armv7l/wheel/pytim-0.8.4-py3.9.egg-info
2021-07-16T11:10:42,969   running install_scripts
2021-07-16T11:10:43,024   creating build/bdist.linux-armv7l/wheel/pytim-0.8.4.dist-info/WHEEL
2021-07-16T11:10:43,027   creating '/tmp/pip-wheel-glejytmf/pytim-0.8.4-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-16T11:10:43,201   adding 'circumradius.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T11:10:43,259   adding 'pytim_dbscan.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T11:10:43,263   adding 'pytim/__init__.py'
2021-07-16T11:10:43,265   adding 'pytim/atoms_maps.py'
2021-07-16T11:10:43,267   adding 'pytim/chacon_tarazona.py'
2021-07-16T11:10:43,269   adding 'pytim/cube.py'
2021-07-16T11:10:43,271   adding 'pytim/gaussian_kde_pbc.py'
2021-07-16T11:10:43,273   adding 'pytim/gitim.py'
2021-07-16T11:10:43,277   adding 'pytim/interface.py'
2021-07-16T11:10:43,280   adding 'pytim/itim.py'
2021-07-16T11:10:43,281   adding 'pytim/messages.py'
2021-07-16T11:10:43,283   adding 'pytim/patches.py'
2021-07-16T11:10:43,285   adding 'pytim/properties.py'
2021-07-16T11:10:43,287   adding 'pytim/sanity_check.py'
2021-07-16T11:10:43,289   adding 'pytim/sasa.py'
2021-07-16T11:10:43,291   adding 'pytim/simple_interface.py'
2021-07-16T11:10:43,294   adding 'pytim/surface.py'
2021-07-16T11:10:43,296   adding 'pytim/utilities.py'
2021-07-16T11:10:43,298   adding 'pytim/utilities_dbscan.py'
2021-07-16T11:10:43,300   adding 'pytim/utilities_geometry.py'
2021-07-16T11:10:43,302   adding 'pytim/utilities_mesh.py'
2021-07-16T11:10:43,303   adding 'pytim/utilities_pbc.py'
2021-07-16T11:10:43,305   adding 'pytim/version.py'
2021-07-16T11:10:43,307   adding 'pytim/vtk.py'
2021-07-16T11:10:43,308   adding 'pytim/wavefront_obj.py'
2021-07-16T11:10:43,311   adding 'pytim/willard_chandler.py'
2021-07-16T11:10:43,312   adding 'pytim/writepdb.py'
2021-07-16T11:10:44,272   adding 'pytim/data/CCL4.H2O.GRO'
2021-07-16T11:10:44,665   adding 'pytim/data/LJ.gro'
2021-07-16T11:10:44,962   adding 'pytim/data/LJ.short.xtc'
2021-07-16T11:10:44,985   adding 'pytim/data/_test_bcc.gro'
2021-07-16T11:10:44,987   adding 'pytim/data/_test_orientation.gro'
2021-07-16T11:10:44,988   adding 'pytim/data/_test_profile.gro'
2021-07-16T11:10:45,796   adding 'pytim/data/antagonistic.gro'
2021-07-16T11:10:46,570   adding 'pytim/data/dppc.gro'
2021-07-16T11:10:46,593   adding 'pytim/data/ffamber03.nonbonded.itp'
2021-07-16T11:10:46,601   adding 'pytim/data/ffcharmm27.nonbonded.itp'
2021-07-16T11:10:46,615   adding 'pytim/data/ffg43a1.nonbonded.itp'
2021-07-16T11:10:46,618   adding 'pytim/data/fullerene.pdb'
2021-07-16T11:10:46,625   adding 'pytim/data/glucose.pdb'
2021-07-16T11:10:47,634   adding 'pytim/data/ilbenzene.gro'
2021-07-16T11:10:47,664   adding 'pytim/data/logo.pdf'
2021-07-16T11:10:47,666   adding 'pytim/data/logo.svg'
2021-07-16T11:10:47,904   adding 'pytim/data/methanol.gro'
2021-07-16T11:10:48,108   adding 'pytim/data/micelle.pdb'
2021-07-16T11:10:48,127   adding 'pytim/data/water-small.gro'
2021-07-16T11:10:48,373   adding 'pytim/data/water.gro'
2021-07-16T11:10:48,496   adding 'pytim/data/water.pdb'
2021-07-16T11:10:48,985   adding 'pytim/data/water.xtc'
2021-07-16T11:10:49,109   adding 'pytim/data/water.xyz'
2021-07-16T11:10:49,172   adding 'pytim/data/water_520K.gro'
2021-07-16T11:10:49,236   adding 'pytim/data/water_550K.gro'
2021-07-16T11:10:49,482   adding 'pytim/data/water_lmp.data'
2021-07-16T11:10:49,556   adding 'pytim/data/water_lmp.xtc'
2021-07-16T11:10:49,564   adding 'pytim/datafiles/__init__.py'
2021-07-16T11:10:49,567   adding 'pytim/observables/__init__.py'
2021-07-16T11:10:49,569   adding 'pytim/observables/basic_observables.py'
2021-07-16T11:10:49,571   adding 'pytim/observables/correlator.py'
2021-07-16T11:10:49,574   adding 'pytim/observables/distributionfunction.py'
2021-07-16T11:10:49,576   adding 'pytim/observables/free_volume.py'
2021-07-16T11:10:49,577   adding 'pytim/observables/intrinsic_distance.py'
2021-07-16T11:10:49,579   adding 'pytim/observables/layer_triangulation.py'
2021-07-16T11:10:49,581   adding 'pytim/observables/local_frame.py'
2021-07-16T11:10:49,583   adding 'pytim/observables/observable.py'
2021-07-16T11:10:49,585   adding 'pytim/observables/orientation.py'
2021-07-16T11:10:49,588   adding 'pytim/observables/profile.py'
2021-07-16T11:10:49,590   adding 'pytim/observables/rdf.py'
2021-07-16T11:10:49,592   adding 'pytim/observables/rdf2d.py'
2021-07-16T11:10:49,595   adding 'pytim-0.8.4.dist-info/METADATA'
2021-07-16T11:10:49,596   adding 'pytim-0.8.4.dist-info/WHEEL'
2021-07-16T11:10:49,597   adding 'pytim-0.8.4.dist-info/top_level.txt'
2021-07-16T11:10:49,599   adding 'pytim-0.8.4.dist-info/RECORD'
2021-07-16T11:10:49,782   removing build/bdist.linux-armv7l/wheel
2021-07-16T11:10:50,433   Building wheel for pytim (setup.py): finished with status 'done'
2021-07-16T11:10:50,609   Created wheel for pytim: filename=pytim-0.8.4-cp39-cp39-linux_armv7l.whl size=14071777 sha256=1a91d6f1843fff1fca1f98fb93274ddbc5d66509dd4b0250c9e07b6de3d2c2bd
2021-07-16T11:10:50,610   Stored in directory: /tmp/pip-ephem-wheel-cache-7u49rbsy/wheels/ab/96/5a/895d570761792f4b4a99457af9b8a6eaf4a09f5abec90cc951
2021-07-16T11:10:50,627 Successfully built pytim
2021-07-16T11:10:51,010 Removed build tracker: '/tmp/pip-req-tracker-64rzzmzj'