2021-07-16T04:41:50,884 Created temporary directory: /tmp/pip-ephem-wheel-cache-xsruoi1t
2021-07-16T04:41:50,887 Created temporary directory: /tmp/pip-req-tracker-48sil7r2
2021-07-16T04:41:50,887 Initialized build tracking at /tmp/pip-req-tracker-48sil7r2
2021-07-16T04:41:50,888 Created build tracker: /tmp/pip-req-tracker-48sil7r2
2021-07-16T04:41:50,888 Entered build tracker: /tmp/pip-req-tracker-48sil7r2
2021-07-16T04:41:50,888 Created temporary directory: /tmp/pip-wheel-uvu6c4dw
2021-07-16T04:41:50,917 1 location(s) to search for versions of pytim:
2021-07-16T04:41:50,917 * https://pypi.org/simple/pytim/
2021-07-16T04:41:50,917 Fetching project page and analyzing links: https://pypi.org/simple/pytim/
2021-07-16T04:41:50,918 Getting page https://pypi.org/simple/pytim/
2021-07-16T04:41:50,919 Found index url https://pypi.org/simple
2021-07-16T04:41:51,100   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
2021-07-16T04:41:51,101   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
2021-07-16T04:41:51,101   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
2021-07-16T04:41:51,102   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
2021-07-16T04:41:51,102   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
2021-07-16T04:41:51,102   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
2021-07-16T04:41:51,102   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
2021-07-16T04:41:51,103   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
2021-07-16T04:41:51,103   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
2021-07-16T04:41:51,103   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
2021-07-16T04:41:51,104   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
2021-07-16T04:41:51,104   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
2021-07-16T04:41:51,104   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
2021-07-16T04:41:51,104   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
2021-07-16T04:41:51,105   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
2021-07-16T04:41:51,105 Skipping link: not a file: https://pypi.org/simple/pytim/
2021-07-16T04:41:51,124 Given no hashes to check 1 links for project 'pytim': discarding no candidates
2021-07-16T04:41:51,143 Collecting pytim==0.8.3
2021-07-16T04:41:51,145   Created temporary directory: /tmp/pip-unpack-o38u67gp
2021-07-16T04:41:53,499   Downloading pytim-0.8.3.tar.gz (13.6 MB)
2021-07-16T04:41:56,128   Added pytim==0.8.3 from https://files.pythonhosted.org/packages/9d/56/916297147f61c10aecaf15469c6e128447f2de417f3647ade801e0e882aa/pytim-0.8.3.tar.gz#sha256=4d844caf3ff61dd781ad9e97ffbbb19dd161770a80cf536edb9feaad2fb88394 to build tracker '/tmp/pip-req-tracker-48sil7r2'
2021-07-16T04:41:56,130     Running setup.py (path:/tmp/pip-wheel-uvu6c4dw/pytim_d8bbd519d0fe4e9a8febd6e9ecbc806a/setup.py) egg_info for package pytim
2021-07-16T04:41:56,131     Created temporary directory: /tmp/pip-pip-egg-info-xne10idu
2021-07-16T04:41:56,131     Running command python setup.py egg_info
2021-07-16T04:41:57,791     running egg_info
2021-07-16T04:41:57,794     creating /tmp/pip-pip-egg-info-xne10idu/pytim.egg-info
2021-07-16T04:41:57,795     writing /tmp/pip-pip-egg-info-xne10idu/pytim.egg-info/PKG-INFO
2021-07-16T04:41:57,797     writing dependency_links to /tmp/pip-pip-egg-info-xne10idu/pytim.egg-info/dependency_links.txt
2021-07-16T04:41:57,799     writing requirements to /tmp/pip-pip-egg-info-xne10idu/pytim.egg-info/requires.txt
2021-07-16T04:41:57,800     writing top-level names to /tmp/pip-pip-egg-info-xne10idu/pytim.egg-info/top_level.txt
2021-07-16T04:41:57,802     writing manifest file '/tmp/pip-pip-egg-info-xne10idu/pytim.egg-info/SOURCES.txt'
2021-07-16T04:41:57,991     reading manifest file '/tmp/pip-pip-egg-info-xne10idu/pytim.egg-info/SOURCES.txt'
2021-07-16T04:41:57,999     writing manifest file '/tmp/pip-pip-egg-info-xne10idu/pytim.egg-info/SOURCES.txt'
2021-07-16T04:41:58,114   Source in /tmp/pip-wheel-uvu6c4dw/pytim_d8bbd519d0fe4e9a8febd6e9ecbc806a has version 0.8.3, which satisfies requirement pytim==0.8.3 from https://files.pythonhosted.org/packages/9d/56/916297147f61c10aecaf15469c6e128447f2de417f3647ade801e0e882aa/pytim-0.8.3.tar.gz#sha256=4d844caf3ff61dd781ad9e97ffbbb19dd161770a80cf536edb9feaad2fb88394
2021-07-16T04:41:58,115   Removed pytim==0.8.3 from https://files.pythonhosted.org/packages/9d/56/916297147f61c10aecaf15469c6e128447f2de417f3647ade801e0e882aa/pytim-0.8.3.tar.gz#sha256=4d844caf3ff61dd781ad9e97ffbbb19dd161770a80cf536edb9feaad2fb88394 from build tracker '/tmp/pip-req-tracker-48sil7r2'
2021-07-16T04:41:58,119 Created temporary directory: /tmp/pip-unpack-mrwpiu17
2021-07-16T04:41:58,120 Building wheels for collected packages: pytim
2021-07-16T04:41:58,124   Created temporary directory: /tmp/pip-wheel-y8gn1z6s
2021-07-16T04:41:58,124   Building wheel for pytim (setup.py): started
2021-07-16T04:41:58,124   Destination directory: /tmp/pip-wheel-y8gn1z6s
2021-07-16T04:41:58,125   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-uvu6c4dw/pytim_d8bbd519d0fe4e9a8febd6e9ecbc806a/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-uvu6c4dw/pytim_d8bbd519d0fe4e9a8febd6e9ecbc806a/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-y8gn1z6s
2021-07-16T04:41:59,734   running bdist_wheel
2021-07-16T04:41:59,739   running build
2021-07-16T04:41:59,740   running build_py
2021-07-16T04:41:59,875   creating build
2021-07-16T04:41:59,875   creating build/lib.linux-armv7l-3.9
2021-07-16T04:41:59,876   creating build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,877   copying pytim/properties.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,879   copying pytim/willard_chandler.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,881   copying pytim/messages.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,883   copying pytim/utilities.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,886   copying pytim/interface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,888   copying pytim/surface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,891   copying pytim/__init__.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,893   copying pytim/wavefront_obj.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,894   copying pytim/utilities_geometry.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,897   copying pytim/utilities_mesh.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,899   copying pytim/atoms_maps.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,901   copying pytim/cube.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,903   copying pytim/simple_interface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,906   copying pytim/gaussian_kde_pbc.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,908   copying pytim/sasa.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,910   copying pytim/utilities_pbc.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,912   copying pytim/patches.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,915   copying pytim/utilities_dbscan.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,917   copying pytim/writepdb.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,919   copying pytim/chacon_tarazona.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,922   copying pytim/sanity_check.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,925   copying pytim/version.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,927   copying pytim/itim.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,929   copying pytim/gitim.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,932   copying pytim/vtk.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-16T04:41:59,935   creating build/lib.linux-armv7l-3.9/pytim/datafiles
2021-07-16T04:41:59,936   copying pytim/datafiles/__init__.py -> build/lib.linux-armv7l-3.9/pytim/datafiles
2021-07-16T04:41:59,941   creating build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,942   copying pytim/observables/local_frame.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,944   copying pytim/observables/__init__.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,947   copying pytim/observables/rdf2d.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,950   copying pytim/observables/rdf.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,953   copying pytim/observables/profile.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,956   copying pytim/observables/correlator.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,959   copying pytim/observables/intrinsic_distance.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,961   copying pytim/observables/observable.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,964   copying pytim/observables/distributionfunction.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,968   copying pytim/observables/layer_triangulation.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,970   copying pytim/observables/orientation.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,972   copying pytim/observables/basic_observables.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,975   copying pytim/observables/free_volume.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-16T04:41:59,982   creating build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:41:59,983   copying pytim/data/fullerene.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:41:59,986   copying pytim/data/logo.svg -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:41:59,990   copying pytim/data/water.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,091   copying pytim/data/water.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,118   copying pytim/data/CCL4.H2O.GRO -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,195   copying pytim/data/dppc.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,248   copying pytim/data/ffg43a1.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,253   copying pytim/data/_test_profile.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,254   copying pytim/data/LJ.short.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,323   copying pytim/data/micelle.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,353   copying pytim/data/ffcharmm27.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,358   copying pytim/data/_test_orientation.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,360   copying pytim/data/water-small.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,363   copying pytim/data/_test_bcc.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,365   copying pytim/data/methanol.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,386   copying pytim/data/water_520K.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,394   copying pytim/data/glucose.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,397   copying pytim/data/ffamber03.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,400   copying pytim/data/water_lmp.data -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,424   copying pytim/data/water.xyz -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,433   copying pytim/data/antagonistic.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,499   copying pytim/data/logo.pdf -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,501   copying pytim/data/water_lmp.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,529   copying pytim/data/ilbenzene.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,609   copying pytim/data/water_550K.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,616   copying pytim/data/LJ.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,648   copying pytim/data/water.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-16T04:42:00,677   running build_ext
2021-07-16T04:42:00,766   cythoning pytim/dbscan_inner.pyx to pytim/dbscan_inner.cpp
2021-07-16T04:42:01,378   /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-uvu6c4dw/pytim_d8bbd519d0fe4e9a8febd6e9ecbc806a/pytim/dbscan_inner.pyx
2021-07-16T04:42:01,378     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-16T04:42:03,017   cythoning pytim/circumradius.pyx to pytim/circumradius.cpp
2021-07-16T04:42:03,023   /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-uvu6c4dw/pytim_d8bbd519d0fe4e9a8febd6e9ecbc806a/pytim/circumradius.pyx
2021-07-16T04:42:03,023     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-16T04:42:17,218   building 'pytim_dbscan' extension
2021-07-16T04:42:17,219   creating build/temp.linux-armv7l-3.9
2021-07-16T04:42:17,219   creating build/temp.linux-armv7l-3.9/pytim
2021-07-16T04:42:17,220   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
2021-07-16T04:42:17,653   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T04:42:17,653                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T04:42:17,653                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T04:42:17,653                    from pytim/dbscan_inner.cpp:644:
2021-07-16T04:42:17,654   /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]
2021-07-16T04:42:17,654      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T04:42:17,654         |  ^~~~~~~
2021-07-16T04:42:21,238   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
2021-07-16T04:42:21,522   building 'circumradius' extension
2021-07-16T04:42:21,522   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
2021-07-16T04:42:21,811   In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-16T04:42:21,811                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-16T04:42:21,811                    from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-16T04:42:21,811                    from pytim/circumradius.cpp:627:
2021-07-16T04:42:21,811   /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]
2021-07-16T04:42:21,811      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-16T04:42:21,812         |  ^~~~~~~
2021-07-16T04:42:22,947   pytim/circumradius.cpp: In function ‘PyObject* __pyx_f_12circumradius__circumradius(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’:
2021-07-16T04:42:22,947   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]
2021-07-16T04:42:22,948    2754 |   for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
2021-07-16T04:42:22,948         |                       ~~~~~~~~~~^~~~~~~~~~~
2021-07-16T04:42:34,420   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
2021-07-16T04:42:34,644   installing to build/bdist.linux-armv7l/wheel
2021-07-16T04:42:34,645   running install
2021-07-16T04:42:34,646   running install_lib
2021-07-16T04:42:34,652   creating build/bdist.linux-armv7l
2021-07-16T04:42:34,652   creating build/bdist.linux-armv7l/wheel
2021-07-16T04:42:34,653   copying build/lib.linux-armv7l-3.9/pytim_dbscan.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2021-07-16T04:42:34,663   creating build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,664   copying build/lib.linux-armv7l-3.9/pytim/properties.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,667   copying build/lib.linux-armv7l-3.9/pytim/willard_chandler.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,669   copying build/lib.linux-armv7l-3.9/pytim/messages.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,671   copying build/lib.linux-armv7l-3.9/pytim/utilities.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,674   copying build/lib.linux-armv7l-3.9/pytim/interface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,677   copying build/lib.linux-armv7l-3.9/pytim/surface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,680   copying build/lib.linux-armv7l-3.9/pytim/__init__.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,682   copying build/lib.linux-armv7l-3.9/pytim/wavefront_obj.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,684   copying build/lib.linux-armv7l-3.9/pytim/utilities_geometry.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,687   copying build/lib.linux-armv7l-3.9/pytim/utilities_mesh.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,689   copying build/lib.linux-armv7l-3.9/pytim/atoms_maps.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,691   copying build/lib.linux-armv7l-3.9/pytim/cube.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,694   creating build/bdist.linux-armv7l/wheel/pytim/datafiles
2021-07-16T04:42:34,695   copying build/lib.linux-armv7l-3.9/pytim/datafiles/__init__.py -> build/bdist.linux-armv7l/wheel/pytim/datafiles
2021-07-16T04:42:34,698   copying build/lib.linux-armv7l-3.9/pytim/simple_interface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,702   creating build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,703   copying build/lib.linux-armv7l-3.9/pytim/observables/local_frame.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,705   copying build/lib.linux-armv7l-3.9/pytim/observables/__init__.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,707   copying build/lib.linux-armv7l-3.9/pytim/observables/rdf2d.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,710   copying build/lib.linux-armv7l-3.9/pytim/observables/rdf.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,713   copying build/lib.linux-armv7l-3.9/pytim/observables/profile.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,715   copying build/lib.linux-armv7l-3.9/pytim/observables/correlator.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,718   copying build/lib.linux-armv7l-3.9/pytim/observables/intrinsic_distance.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,720   copying build/lib.linux-armv7l-3.9/pytim/observables/observable.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,723   copying build/lib.linux-armv7l-3.9/pytim/observables/distributionfunction.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,726   copying build/lib.linux-armv7l-3.9/pytim/observables/layer_triangulation.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,728   copying build/lib.linux-armv7l-3.9/pytim/observables/orientation.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,731   copying build/lib.linux-armv7l-3.9/pytim/observables/basic_observables.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,733   copying build/lib.linux-armv7l-3.9/pytim/observables/free_volume.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-16T04:42:34,736   copying build/lib.linux-armv7l-3.9/pytim/gaussian_kde_pbc.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,738   copying build/lib.linux-armv7l-3.9/pytim/sasa.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,741   copying build/lib.linux-armv7l-3.9/pytim/utilities_pbc.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,743   copying build/lib.linux-armv7l-3.9/pytim/patches.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,745   copying build/lib.linux-armv7l-3.9/pytim/utilities_dbscan.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,747   copying build/lib.linux-armv7l-3.9/pytim/writepdb.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,750   copying build/lib.linux-armv7l-3.9/pytim/chacon_tarazona.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:34,754   creating build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:34,755   copying build/lib.linux-armv7l-3.9/pytim/data/fullerene.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:34,757   copying build/lib.linux-armv7l-3.9/pytim/data/logo.svg -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:34,760   copying build/lib.linux-armv7l-3.9/pytim/data/water.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:34,860   copying build/lib.linux-armv7l-3.9/pytim/data/water.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:34,879   copying build/lib.linux-armv7l-3.9/pytim/data/CCL4.H2O.GRO -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:34,949   copying build/lib.linux-armv7l-3.9/pytim/data/dppc.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,018   copying build/lib.linux-armv7l-3.9/pytim/data/ffg43a1.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,022   copying build/lib.linux-armv7l-3.9/pytim/data/_test_profile.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,024   copying build/lib.linux-armv7l-3.9/pytim/data/LJ.short.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,087   copying build/lib.linux-armv7l-3.9/pytim/data/micelle.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,125   copying build/lib.linux-armv7l-3.9/pytim/data/ffcharmm27.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,132   copying build/lib.linux-armv7l-3.9/pytim/data/_test_orientation.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,134   copying build/lib.linux-armv7l-3.9/pytim/data/water-small.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,137   copying build/lib.linux-armv7l-3.9/pytim/data/_test_bcc.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,138   copying build/lib.linux-armv7l-3.9/pytim/data/methanol.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,167   copying build/lib.linux-armv7l-3.9/pytim/data/water_520K.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,175   copying build/lib.linux-armv7l-3.9/pytim/data/glucose.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,178   copying build/lib.linux-armv7l-3.9/pytim/data/ffamber03.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,180   copying build/lib.linux-armv7l-3.9/pytim/data/water_lmp.data -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,207   copying build/lib.linux-armv7l-3.9/pytim/data/water.xyz -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,215   copying build/lib.linux-armv7l-3.9/pytim/data/antagonistic.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,277   copying build/lib.linux-armv7l-3.9/pytim/data/logo.pdf -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,278   copying build/lib.linux-armv7l-3.9/pytim/data/water_lmp.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,293   copying build/lib.linux-armv7l-3.9/pytim/data/ilbenzene.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,376   copying build/lib.linux-armv7l-3.9/pytim/data/water_550K.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,386   copying build/lib.linux-armv7l-3.9/pytim/data/LJ.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,424   copying build/lib.linux-armv7l-3.9/pytim/data/water.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-16T04:42:35,450   copying build/lib.linux-armv7l-3.9/pytim/sanity_check.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:35,454   copying build/lib.linux-armv7l-3.9/pytim/version.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:35,456   copying build/lib.linux-armv7l-3.9/pytim/itim.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:35,459   copying build/lib.linux-armv7l-3.9/pytim/gitim.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:35,462   copying build/lib.linux-armv7l-3.9/pytim/vtk.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-16T04:42:35,465   copying build/lib.linux-armv7l-3.9/circumradius.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2021-07-16T04:42:35,491   running install_egg_info
2021-07-16T04:42:35,515   running egg_info
2021-07-16T04:42:35,516   writing pytim.egg-info/PKG-INFO
2021-07-16T04:42:35,518   writing dependency_links to pytim.egg-info/dependency_links.txt
2021-07-16T04:42:35,519   writing requirements to pytim.egg-info/requires.txt
2021-07-16T04:42:35,521   writing top-level names to pytim.egg-info/top_level.txt
2021-07-16T04:42:35,570   reading manifest file 'pytim.egg-info/SOURCES.txt'
2021-07-16T04:42:35,583   writing manifest file 'pytim.egg-info/SOURCES.txt'
2021-07-16T04:42:35,585   Copying pytim.egg-info to build/bdist.linux-armv7l/wheel/pytim-0.8.3-py3.9.egg-info
2021-07-16T04:42:35,596   running install_scripts
2021-07-16T04:42:35,651   creating build/bdist.linux-armv7l/wheel/pytim-0.8.3.dist-info/WHEEL
2021-07-16T04:42:35,654   creating '/tmp/pip-wheel-y8gn1z6s/pytim-0.8.3-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-16T04:42:35,828   adding 'circumradius.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T04:42:35,884   adding 'pytim_dbscan.cpython-39-arm-linux-gnueabihf.so'
2021-07-16T04:42:35,888   adding 'pytim/__init__.py'
2021-07-16T04:42:35,890   adding 'pytim/atoms_maps.py'
2021-07-16T04:42:35,891   adding 'pytim/chacon_tarazona.py'
2021-07-16T04:42:35,893   adding 'pytim/cube.py'
2021-07-16T04:42:35,894   adding 'pytim/gaussian_kde_pbc.py'
2021-07-16T04:42:35,896   adding 'pytim/gitim.py'
2021-07-16T04:42:35,899   adding 'pytim/interface.py'
2021-07-16T04:42:35,902   adding 'pytim/itim.py'
2021-07-16T04:42:35,903   adding 'pytim/messages.py'
2021-07-16T04:42:35,905   adding 'pytim/patches.py'
2021-07-16T04:42:35,906   adding 'pytim/properties.py'
2021-07-16T04:42:35,908   adding 'pytim/sanity_check.py'
2021-07-16T04:42:35,910   adding 'pytim/sasa.py'
2021-07-16T04:42:35,911   adding 'pytim/simple_interface.py'
2021-07-16T04:42:35,913   adding 'pytim/surface.py'
2021-07-16T04:42:35,915   adding 'pytim/utilities.py'
2021-07-16T04:42:35,917   adding 'pytim/utilities_dbscan.py'
2021-07-16T04:42:35,919   adding 'pytim/utilities_geometry.py'
2021-07-16T04:42:35,920   adding 'pytim/utilities_mesh.py'
2021-07-16T04:42:35,921   adding 'pytim/utilities_pbc.py'
2021-07-16T04:42:35,922   adding 'pytim/version.py'
2021-07-16T04:42:35,924   adding 'pytim/vtk.py'
2021-07-16T04:42:35,925   adding 'pytim/wavefront_obj.py'
2021-07-16T04:42:35,927   adding 'pytim/willard_chandler.py'
2021-07-16T04:42:35,928   adding 'pytim/writepdb.py'
2021-07-16T04:42:36,890   adding 'pytim/data/CCL4.H2O.GRO'
2021-07-16T04:42:37,282   adding 'pytim/data/LJ.gro'
2021-07-16T04:42:37,582   adding 'pytim/data/LJ.short.xtc'
2021-07-16T04:42:37,604   adding 'pytim/data/_test_bcc.gro'
2021-07-16T04:42:37,605   adding 'pytim/data/_test_orientation.gro'
2021-07-16T04:42:37,606   adding 'pytim/data/_test_profile.gro'
2021-07-16T04:42:38,426   adding 'pytim/data/antagonistic.gro'
2021-07-16T04:42:39,216   adding 'pytim/data/dppc.gro'
2021-07-16T04:42:39,238   adding 'pytim/data/ffamber03.nonbonded.itp'
2021-07-16T04:42:39,246   adding 'pytim/data/ffcharmm27.nonbonded.itp'
2021-07-16T04:42:39,259   adding 'pytim/data/ffg43a1.nonbonded.itp'
2021-07-16T04:42:39,262   adding 'pytim/data/fullerene.pdb'
2021-07-16T04:42:39,269   adding 'pytim/data/glucose.pdb'
2021-07-16T04:42:40,275   adding 'pytim/data/ilbenzene.gro'
2021-07-16T04:42:40,305   adding 'pytim/data/logo.pdf'
2021-07-16T04:42:40,307   adding 'pytim/data/logo.svg'
2021-07-16T04:42:40,555   adding 'pytim/data/methanol.gro'
2021-07-16T04:42:40,759   adding 'pytim/data/micelle.pdb'
2021-07-16T04:42:40,776   adding 'pytim/data/water-small.gro'
2021-07-16T04:42:41,019   adding 'pytim/data/water.gro'
2021-07-16T04:42:41,141   adding 'pytim/data/water.pdb'
2021-07-16T04:42:41,636   adding 'pytim/data/water.xtc'
2021-07-16T04:42:41,758   adding 'pytim/data/water.xyz'
2021-07-16T04:42:41,821   adding 'pytim/data/water_520K.gro'
2021-07-16T04:42:41,884   adding 'pytim/data/water_550K.gro'
2021-07-16T04:42:42,130   adding 'pytim/data/water_lmp.data'
2021-07-16T04:42:42,205   adding 'pytim/data/water_lmp.xtc'
2021-07-16T04:42:42,213   adding 'pytim/datafiles/__init__.py'
2021-07-16T04:42:42,215   adding 'pytim/observables/__init__.py'
2021-07-16T04:42:42,217   adding 'pytim/observables/basic_observables.py'
2021-07-16T04:42:42,219   adding 'pytim/observables/correlator.py'
2021-07-16T04:42:42,222   adding 'pytim/observables/distributionfunction.py'
2021-07-16T04:42:42,224   adding 'pytim/observables/free_volume.py'
2021-07-16T04:42:42,225   adding 'pytim/observables/intrinsic_distance.py'
2021-07-16T04:42:42,226   adding 'pytim/observables/layer_triangulation.py'
2021-07-16T04:42:42,228   adding 'pytim/observables/local_frame.py'
2021-07-16T04:42:42,230   adding 'pytim/observables/observable.py'
2021-07-16T04:42:42,231   adding 'pytim/observables/orientation.py'
2021-07-16T04:42:42,233   adding 'pytim/observables/profile.py'
2021-07-16T04:42:42,235   adding 'pytim/observables/rdf.py'
2021-07-16T04:42:42,236   adding 'pytim/observables/rdf2d.py'
2021-07-16T04:42:42,239   adding 'pytim-0.8.3.dist-info/METADATA'
2021-07-16T04:42:42,240   adding 'pytim-0.8.3.dist-info/WHEEL'
2021-07-16T04:42:42,241   adding 'pytim-0.8.3.dist-info/top_level.txt'
2021-07-16T04:42:42,242   adding 'pytim-0.8.3.dist-info/RECORD'
2021-07-16T04:42:42,444   removing build/bdist.linux-armv7l/wheel
2021-07-16T04:42:43,090   Building wheel for pytim (setup.py): finished with status 'done'
2021-07-16T04:42:43,265   Created wheel for pytim: filename=pytim-0.8.3-cp39-cp39-linux_armv7l.whl size=14070599 sha256=8e688e92d676d7876cd12baeadae97713f81f93e06f4913e3726aa460106d8eb
2021-07-16T04:42:43,265   Stored in directory: /tmp/pip-ephem-wheel-cache-xsruoi1t/wheels/d7/6f/51/7563fd16e1d9adeae82f2e250305187b62977ac6145b5d6665
2021-07-16T04:42:43,283 Successfully built pytim
2021-07-16T04:42:43,715 Removed build tracker: '/tmp/pip-req-tracker-48sil7r2'