2021-07-13T03:38:32,151 Created temporary directory: /tmp/pip-ephem-wheel-cache-4wo676vw
2021-07-13T03:38:32,154 Created temporary directory: /tmp/pip-req-tracker-j5ry19i7
2021-07-13T03:38:32,154 Initialized build tracking at /tmp/pip-req-tracker-j5ry19i7
2021-07-13T03:38:32,154 Created build tracker: /tmp/pip-req-tracker-j5ry19i7
2021-07-13T03:38:32,155 Entered build tracker: /tmp/pip-req-tracker-j5ry19i7
2021-07-13T03:38:32,155 Created temporary directory: /tmp/pip-wheel-uqehpw3s
2021-07-13T03:38:32,184 1 location(s) to search for versions of pytim:
2021-07-13T03:38:32,184 * https://pypi.org/simple/pytim/
2021-07-13T03:38:32,185 Fetching project page and analyzing links: https://pypi.org/simple/pytim/
2021-07-13T03:38:32,185 Getting page https://pypi.org/simple/pytim/
2021-07-13T03:38:32,187 Found index url https://pypi.org/simple
2021-07-13T03:38:32,281   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
2021-07-13T03:38:32,281   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
2021-07-13T03:38:32,281   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
2021-07-13T03:38:32,282   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
2021-07-13T03:38:32,282   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
2021-07-13T03:38:32,282   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
2021-07-13T03:38:32,282   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
2021-07-13T03:38:32,283   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
2021-07-13T03:38:32,283   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
2021-07-13T03:38:32,283   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
2021-07-13T03:38:32,284   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
2021-07-13T03:38:32,284   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
2021-07-13T03:38:32,284   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
2021-07-13T03:38:32,284   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
2021-07-13T03:38:32,285   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
2021-07-13T03:38:32,285 Skipping link: not a file: https://pypi.org/simple/pytim/
2021-07-13T03:38:32,305 Given no hashes to check 1 links for project 'pytim': discarding no candidates
2021-07-13T03:38:32,323 Collecting pytim==0.8.0
2021-07-13T03:38:32,325   Created temporary directory: /tmp/pip-unpack-w2bpoz2z
2021-07-13T03:38:33,328   Downloading pytim-0.8.0.tar.gz (12.7 MB)
2021-07-13T03:38:35,518   Added pytim==0.8.0 from https://files.pythonhosted.org/packages/e0/b8/b32af8aacd0a1b96e92accffa4a644e983f978cacc31e45037619246e763/pytim-0.8.0.tar.gz#sha256=d5a65559becebb30fb1ae7b3b769a10cffa484539c2fb246f8f25271b66dc7eb to build tracker '/tmp/pip-req-tracker-j5ry19i7'
2021-07-13T03:38:35,519     Running setup.py (path:/tmp/pip-wheel-uqehpw3s/pytim_d259c20cf56c45f3989b430d1d5013a1/setup.py) egg_info for package pytim
2021-07-13T03:38:35,520     Created temporary directory: /tmp/pip-pip-egg-info-nogaazfe
2021-07-13T03:38:35,521     Running command python setup.py egg_info
2021-07-13T03:38:37,101     running egg_info
2021-07-13T03:38:37,104     creating /tmp/pip-pip-egg-info-nogaazfe/pytim.egg-info
2021-07-13T03:38:37,105     writing /tmp/pip-pip-egg-info-nogaazfe/pytim.egg-info/PKG-INFO
2021-07-13T03:38:37,108     writing dependency_links to /tmp/pip-pip-egg-info-nogaazfe/pytim.egg-info/dependency_links.txt
2021-07-13T03:38:37,110     writing requirements to /tmp/pip-pip-egg-info-nogaazfe/pytim.egg-info/requires.txt
2021-07-13T03:38:37,111     writing top-level names to /tmp/pip-pip-egg-info-nogaazfe/pytim.egg-info/top_level.txt
2021-07-13T03:38:37,113     writing manifest file '/tmp/pip-pip-egg-info-nogaazfe/pytim.egg-info/SOURCES.txt'
2021-07-13T03:38:37,268     reading manifest file '/tmp/pip-pip-egg-info-nogaazfe/pytim.egg-info/SOURCES.txt'
2021-07-13T03:38:37,273     writing manifest file '/tmp/pip-pip-egg-info-nogaazfe/pytim.egg-info/SOURCES.txt'
2021-07-13T03:38:37,370   Source in /tmp/pip-wheel-uqehpw3s/pytim_d259c20cf56c45f3989b430d1d5013a1 has version 0.8.0, which satisfies requirement pytim==0.8.0 from https://files.pythonhosted.org/packages/e0/b8/b32af8aacd0a1b96e92accffa4a644e983f978cacc31e45037619246e763/pytim-0.8.0.tar.gz#sha256=d5a65559becebb30fb1ae7b3b769a10cffa484539c2fb246f8f25271b66dc7eb
2021-07-13T03:38:37,371   Removed pytim==0.8.0 from https://files.pythonhosted.org/packages/e0/b8/b32af8aacd0a1b96e92accffa4a644e983f978cacc31e45037619246e763/pytim-0.8.0.tar.gz#sha256=d5a65559becebb30fb1ae7b3b769a10cffa484539c2fb246f8f25271b66dc7eb from build tracker '/tmp/pip-req-tracker-j5ry19i7'
2021-07-13T03:38:37,375 Created temporary directory: /tmp/pip-unpack-cm1mmbbb
2021-07-13T03:38:37,376 Building wheels for collected packages: pytim
2021-07-13T03:38:37,379   Created temporary directory: /tmp/pip-wheel-38rc49sj
2021-07-13T03:38:37,380   Building wheel for pytim (setup.py): started
2021-07-13T03:38:37,380   Destination directory: /tmp/pip-wheel-38rc49sj
2021-07-13T03:38:37,381   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-uqehpw3s/pytim_d259c20cf56c45f3989b430d1d5013a1/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-uqehpw3s/pytim_d259c20cf56c45f3989b430d1d5013a1/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-38rc49sj
2021-07-13T03:38:38,893   running bdist_wheel
2021-07-13T03:38:38,899   running build
2021-07-13T03:38:38,899   running build_py
2021-07-13T03:38:39,034   creating build
2021-07-13T03:38:39,035   creating build/lib.linux-armv7l-3.9
2021-07-13T03:38:39,035   creating build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,036   copying pytim/vtk.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,038   copying pytim/pdb.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,040   copying pytim/simple_interface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,043   copying pytim/utilities_dbscan.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,044   copying pytim/utilities_geometry.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,046   copying pytim/willard_chandler.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,049   copying pytim/cube.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,051   copying pytim/atoms_maps.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,053   copying pytim/wavefront_obj.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,055   copying pytim/surface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,057   copying pytim/sanity_check.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,060   copying pytim/patches.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,062   copying pytim/utilities_pbc.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,064   copying pytim/__init__.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,065   copying pytim/messages.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,067   copying pytim/chacon_tarazona.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,070   copying pytim/gaussian_kde_pbc.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,072   copying pytim/utilities.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,074   copying pytim/utilities_mesh.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,076   copying pytim/version.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,078   copying pytim/properties.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,080   copying pytim/interface.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,083   copying pytim/itim.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,085   copying pytim/gitim.py -> build/lib.linux-armv7l-3.9/pytim
2021-07-13T03:38:39,088   creating build/lib.linux-armv7l-3.9/pytim/datafiles
2021-07-13T03:38:39,089   copying pytim/datafiles/__init__.py -> build/lib.linux-armv7l-3.9/pytim/datafiles
2021-07-13T03:38:39,093   creating build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,094   copying pytim/observables/profile.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,097   copying pytim/observables/layer_triangulation.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,099   copying pytim/observables/correlator.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,101   copying pytim/observables/free_volume.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,104   copying pytim/observables/__init__.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,106   copying pytim/observables/intrinsic_distance.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,107   copying pytim/observables/orientation.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,109   copying pytim/observables/rdf.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,112   copying pytim/observables/observable.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,114   copying pytim/observables/basic_observables.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,116   copying pytim/observables/rdf2d.py -> build/lib.linux-armv7l-3.9/pytim/observables
2021-07-13T03:38:39,121   creating build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,122   copying pytim/data/CCL4.H2O.GRO -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,210   copying pytim/data/water_520K.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,216   copying pytim/data/LJ.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,255   copying pytim/data/logo.svg -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,257   copying pytim/data/water.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,353   copying pytim/data/fullerene.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,355   copying pytim/data/_test_profile.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,358   copying pytim/data/water.xyz -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,365   copying pytim/data/ffcharmm27.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,370   copying pytim/data/dppc.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,421   copying pytim/data/water.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,444   copying pytim/data/ilbenzene.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,522   copying pytim/data/water_lmp.data -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,543   copying pytim/data/_test_bcc.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,545   copying pytim/data/water_550K.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,554   copying pytim/data/water.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,582   copying pytim/data/LJ.short.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,642   copying pytim/data/ffg43a1.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,646   copying pytim/data/water-small.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,649   copying pytim/data/ffamber03.nonbonded.itp -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,652   copying pytim/data/glucose.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,656   copying pytim/data/logo.pdf -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,658   copying pytim/data/_test_orientation.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,661   copying pytim/data/methanol.gro -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,681   copying pytim/data/micelle.pdb -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,716   copying pytim/data/water_lmp.xtc -> build/lib.linux-armv7l-3.9/pytim/data
2021-07-13T03:38:39,735   running build_ext
2021-07-13T03:38:39,828   cythoning pytim/dbscan_inner.pyx to pytim/dbscan_inner.cpp
2021-07-13T03:38:40,430   /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-uqehpw3s/pytim_d259c20cf56c45f3989b430d1d5013a1/pytim/dbscan_inner.pyx
2021-07-13T03:38:40,430     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-13T03:38:41,997   cythoning pytim/circumradius.pyx to pytim/circumradius.cpp
2021-07-13T03:38:42,002   /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-uqehpw3s/pytim_d259c20cf56c45f3989b430d1d5013a1/pytim/circumradius.pyx
2021-07-13T03:38:42,003     tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-13T03:38:56,401   building 'pytim_dbscan' extension
2021-07-13T03:38:56,402   creating build/temp.linux-armv7l-3.9
2021-07-13T03:38:56,402   creating build/temp.linux-armv7l-3.9/pytim
2021-07-13T03:38:56,403   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c pytim/dbscan_inner.cpp -o build/temp.linux-armv7l-3.9/pytim/dbscan_inner.o
2021-07-13T03:38:56,847   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-13T03:38:56,848                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-13T03:38:56,848                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-13T03:38:56,848                    from pytim/dbscan_inner.cpp:644:
2021-07-13T03:38:56,848   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-13T03:38:56,848      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-13T03:38:56,849         |  ^~~~~~~
2021-07-13T03:39:00,449   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
2021-07-13T03:39:00,731   building 'circumradius' extension
2021-07-13T03:39:00,732   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c pytim/circumradius.cpp -o build/temp.linux-armv7l-3.9/pytim/circumradius.o
2021-07-13T03:39:01,020   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-13T03:39:01,021                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-13T03:39:01,021                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-13T03:39:01,021                    from pytim/circumradius.cpp:627:
2021-07-13T03:39:01,021   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-13T03:39:01,021      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-13T03:39:01,021         |  ^~~~~~~
2021-07-13T03:39:02,209   pytim/circumradius.cpp: In function ‘PyObject* __pyx_f_12circumradius__circumradius(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice)’:
2021-07-13T03:39:02,210   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]
2021-07-13T03:39:02,210    2754 |   for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
2021-07-13T03:39:02,210         |                       ~~~~~~~~~~^~~~~~~~~~~
2021-07-13T03:39:13,717   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
2021-07-13T03:39:13,947   installing to build/bdist.linux-armv7l/wheel
2021-07-13T03:39:13,948   running install
2021-07-13T03:39:13,949   running install_lib
2021-07-13T03:39:13,955   creating build/bdist.linux-armv7l
2021-07-13T03:39:13,955   creating build/bdist.linux-armv7l/wheel
2021-07-13T03:39:13,958   creating build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,959   copying build/lib.linux-armv7l-3.9/pytim/vtk.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,962   copying build/lib.linux-armv7l-3.9/pytim/pdb.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,964   copying build/lib.linux-armv7l-3.9/pytim/simple_interface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,967   copying build/lib.linux-armv7l-3.9/pytim/utilities_dbscan.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,969   copying build/lib.linux-armv7l-3.9/pytim/utilities_geometry.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,971   copying build/lib.linux-armv7l-3.9/pytim/willard_chandler.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,974   copying build/lib.linux-armv7l-3.9/pytim/cube.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,977   creating build/bdist.linux-armv7l/wheel/pytim/datafiles
2021-07-13T03:39:13,977   copying build/lib.linux-armv7l-3.9/pytim/datafiles/__init__.py -> build/bdist.linux-armv7l/wheel/pytim/datafiles
2021-07-13T03:39:13,980   copying build/lib.linux-armv7l-3.9/pytim/atoms_maps.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,983   copying build/lib.linux-armv7l-3.9/pytim/wavefront_obj.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,984   copying build/lib.linux-armv7l-3.9/pytim/surface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,987   copying build/lib.linux-armv7l-3.9/pytim/sanity_check.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,989   copying build/lib.linux-armv7l-3.9/pytim/patches.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,991   copying build/lib.linux-armv7l-3.9/pytim/utilities_pbc.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,993   copying build/lib.linux-armv7l-3.9/pytim/__init__.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,995   copying build/lib.linux-armv7l-3.9/pytim/messages.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:13,997   copying build/lib.linux-armv7l-3.9/pytim/chacon_tarazona.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,000   copying build/lib.linux-armv7l-3.9/pytim/gaussian_kde_pbc.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,002   copying build/lib.linux-armv7l-3.9/pytim/utilities.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,004   copying build/lib.linux-armv7l-3.9/pytim/utilities_mesh.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,007   creating build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,008   copying build/lib.linux-armv7l-3.9/pytim/data/CCL4.H2O.GRO -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,069   copying build/lib.linux-armv7l-3.9/pytim/data/water_520K.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,076   copying build/lib.linux-armv7l-3.9/pytim/data/LJ.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,116   copying build/lib.linux-armv7l-3.9/pytim/data/logo.svg -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,118   copying build/lib.linux-armv7l-3.9/pytim/data/water.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,211   copying build/lib.linux-armv7l-3.9/pytim/data/fullerene.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,213   copying build/lib.linux-armv7l-3.9/pytim/data/_test_profile.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,215   copying build/lib.linux-armv7l-3.9/pytim/data/water.xyz -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,223   copying build/lib.linux-armv7l-3.9/pytim/data/ffcharmm27.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,231   copying build/lib.linux-armv7l-3.9/pytim/data/dppc.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,288   copying build/lib.linux-armv7l-3.9/pytim/data/water.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,315   copying build/lib.linux-armv7l-3.9/pytim/data/ilbenzene.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,385   copying build/lib.linux-armv7l-3.9/pytim/data/water_lmp.data -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,408   copying build/lib.linux-armv7l-3.9/pytim/data/_test_bcc.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,410   copying build/lib.linux-armv7l-3.9/pytim/data/water_550K.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,417   copying build/lib.linux-armv7l-3.9/pytim/data/water.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,442   copying build/lib.linux-armv7l-3.9/pytim/data/LJ.short.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,503   copying build/lib.linux-armv7l-3.9/pytim/data/ffg43a1.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,507   copying build/lib.linux-armv7l-3.9/pytim/data/water-small.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,510   copying build/lib.linux-armv7l-3.9/pytim/data/ffamber03.nonbonded.itp -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,512   copying build/lib.linux-armv7l-3.9/pytim/data/glucose.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,516   copying build/lib.linux-armv7l-3.9/pytim/data/logo.pdf -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,518   copying build/lib.linux-armv7l-3.9/pytim/data/_test_orientation.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,520   copying build/lib.linux-armv7l-3.9/pytim/data/methanol.gro -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,548   copying build/lib.linux-armv7l-3.9/pytim/data/micelle.pdb -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,579   copying build/lib.linux-armv7l-3.9/pytim/data/water_lmp.xtc -> build/bdist.linux-armv7l/wheel/pytim/data
2021-07-13T03:39:14,595   copying build/lib.linux-armv7l-3.9/pytim/version.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,597   copying build/lib.linux-armv7l-3.9/pytim/properties.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,599   copying build/lib.linux-armv7l-3.9/pytim/interface.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,602   copying build/lib.linux-armv7l-3.9/pytim/itim.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,605   copying build/lib.linux-armv7l-3.9/pytim/gitim.py -> build/bdist.linux-armv7l/wheel/pytim
2021-07-13T03:39:14,608   creating build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,609   copying build/lib.linux-armv7l-3.9/pytim/observables/profile.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,612   copying build/lib.linux-armv7l-3.9/pytim/observables/layer_triangulation.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,613   copying build/lib.linux-armv7l-3.9/pytim/observables/correlator.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,616   copying build/lib.linux-armv7l-3.9/pytim/observables/free_volume.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,619   copying build/lib.linux-armv7l-3.9/pytim/observables/__init__.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,621   copying build/lib.linux-armv7l-3.9/pytim/observables/intrinsic_distance.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,623   copying build/lib.linux-armv7l-3.9/pytim/observables/orientation.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,625   copying build/lib.linux-armv7l-3.9/pytim/observables/rdf.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,628   copying build/lib.linux-armv7l-3.9/pytim/observables/observable.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,630   copying build/lib.linux-armv7l-3.9/pytim/observables/basic_observables.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,633   copying build/lib.linux-armv7l-3.9/pytim/observables/rdf2d.py -> build/bdist.linux-armv7l/wheel/pytim/observables
2021-07-13T03:39:14,636   copying build/lib.linux-armv7l-3.9/pytim_dbscan.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2021-07-13T03:39:14,645   copying build/lib.linux-armv7l-3.9/circumradius.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel
2021-07-13T03:39:14,669   running install_egg_info
2021-07-13T03:39:14,694   running egg_info
2021-07-13T03:39:14,696   writing pytim.egg-info/PKG-INFO
2021-07-13T03:39:14,698   writing dependency_links to pytim.egg-info/dependency_links.txt
2021-07-13T03:39:14,700   writing requirements to pytim.egg-info/requires.txt
2021-07-13T03:39:14,701   writing top-level names to pytim.egg-info/top_level.txt
2021-07-13T03:39:14,717   reading manifest file 'pytim.egg-info/SOURCES.txt'
2021-07-13T03:39:14,726   writing manifest file 'pytim.egg-info/SOURCES.txt'
2021-07-13T03:39:14,727   Copying pytim.egg-info to build/bdist.linux-armv7l/wheel/pytim-0.8.0-py3.9.egg-info
2021-07-13T03:39:14,738   running install_scripts
2021-07-13T03:39:14,791   creating build/bdist.linux-armv7l/wheel/pytim-0.8.0.dist-info/WHEEL
2021-07-13T03:39:14,794   creating '/tmp/pip-wheel-38rc49sj/pytim-0.8.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-13T03:39:14,969   adding 'circumradius.cpython-39-arm-linux-gnueabihf.so'
2021-07-13T03:39:15,025   adding 'pytim_dbscan.cpython-39-arm-linux-gnueabihf.so'
2021-07-13T03:39:15,029   adding 'pytim/__init__.py'
2021-07-13T03:39:15,031   adding 'pytim/atoms_maps.py'
2021-07-13T03:39:15,033   adding 'pytim/chacon_tarazona.py'
2021-07-13T03:39:15,034   adding 'pytim/cube.py'
2021-07-13T03:39:15,035   adding 'pytim/gaussian_kde_pbc.py'
2021-07-13T03:39:15,037   adding 'pytim/gitim.py'
2021-07-13T03:39:15,040   adding 'pytim/interface.py'
2021-07-13T03:39:15,043   adding 'pytim/itim.py'
2021-07-13T03:39:15,044   adding 'pytim/messages.py'
2021-07-13T03:39:15,046   adding 'pytim/patches.py'
2021-07-13T03:39:15,047   adding 'pytim/pdb.py'
2021-07-13T03:39:15,049   adding 'pytim/properties.py'
2021-07-13T03:39:15,051   adding 'pytim/sanity_check.py'
2021-07-13T03:39:15,052   adding 'pytim/simple_interface.py'
2021-07-13T03:39:15,054   adding 'pytim/surface.py'
2021-07-13T03:39:15,056   adding 'pytim/utilities.py'
2021-07-13T03:39:15,058   adding 'pytim/utilities_dbscan.py'
2021-07-13T03:39:15,059   adding 'pytim/utilities_geometry.py'
2021-07-13T03:39:15,060   adding 'pytim/utilities_mesh.py'
2021-07-13T03:39:15,062   adding 'pytim/utilities_pbc.py'
2021-07-13T03:39:15,063   adding 'pytim/version.py'
2021-07-13T03:39:15,064   adding 'pytim/vtk.py'
2021-07-13T03:39:15,065   adding 'pytim/wavefront_obj.py'
2021-07-13T03:39:15,067   adding 'pytim/willard_chandler.py'
2021-07-13T03:39:16,029   adding 'pytim/data/CCL4.H2O.GRO'
2021-07-13T03:39:16,422   adding 'pytim/data/LJ.gro'
2021-07-13T03:39:16,717   adding 'pytim/data/LJ.short.xtc'
2021-07-13T03:39:16,740   adding 'pytim/data/_test_bcc.gro'
2021-07-13T03:39:16,741   adding 'pytim/data/_test_orientation.gro'
2021-07-13T03:39:16,742   adding 'pytim/data/_test_profile.gro'
2021-07-13T03:39:17,491   adding 'pytim/data/dppc.gro'
2021-07-13T03:39:17,513   adding 'pytim/data/ffamber03.nonbonded.itp'
2021-07-13T03:39:17,521   adding 'pytim/data/ffcharmm27.nonbonded.itp'
2021-07-13T03:39:17,533   adding 'pytim/data/ffg43a1.nonbonded.itp'
2021-07-13T03:39:17,535   adding 'pytim/data/fullerene.pdb'
2021-07-13T03:39:17,541   adding 'pytim/data/glucose.pdb'
2021-07-13T03:39:18,545   adding 'pytim/data/ilbenzene.gro'
2021-07-13T03:39:18,575   adding 'pytim/data/logo.pdf'
2021-07-13T03:39:18,577   adding 'pytim/data/logo.svg'
2021-07-13T03:39:18,814   adding 'pytim/data/methanol.gro'
2021-07-13T03:39:19,019   adding 'pytim/data/micelle.pdb'
2021-07-13T03:39:19,036   adding 'pytim/data/water-small.gro'
2021-07-13T03:39:19,280   adding 'pytim/data/water.gro'
2021-07-13T03:39:19,402   adding 'pytim/data/water.pdb'
2021-07-13T03:39:19,890   adding 'pytim/data/water.xtc'
2021-07-13T03:39:20,014   adding 'pytim/data/water.xyz'
2021-07-13T03:39:20,077   adding 'pytim/data/water_520K.gro'
2021-07-13T03:39:20,140   adding 'pytim/data/water_550K.gro'
2021-07-13T03:39:20,386   adding 'pytim/data/water_lmp.data'
2021-07-13T03:39:20,460   adding 'pytim/data/water_lmp.xtc'
2021-07-13T03:39:20,468   adding 'pytim/datafiles/__init__.py'
2021-07-13T03:39:20,469   adding 'pytim/observables/__init__.py'
2021-07-13T03:39:20,471   adding 'pytim/observables/basic_observables.py'
2021-07-13T03:39:20,473   adding 'pytim/observables/correlator.py'
2021-07-13T03:39:20,475   adding 'pytim/observables/free_volume.py'
2021-07-13T03:39:20,476   adding 'pytim/observables/intrinsic_distance.py'
2021-07-13T03:39:20,477   adding 'pytim/observables/layer_triangulation.py'
2021-07-13T03:39:20,478   adding 'pytim/observables/observable.py'
2021-07-13T03:39:20,480   adding 'pytim/observables/orientation.py'
2021-07-13T03:39:20,482   adding 'pytim/observables/profile.py'
2021-07-13T03:39:20,484   adding 'pytim/observables/rdf.py'
2021-07-13T03:39:20,485   adding 'pytim/observables/rdf2d.py'
2021-07-13T03:39:20,487   adding 'pytim-0.8.0.dist-info/METADATA'
2021-07-13T03:39:20,488   adding 'pytim-0.8.0.dist-info/WHEEL'
2021-07-13T03:39:20,489   adding 'pytim-0.8.0.dist-info/top_level.txt'
2021-07-13T03:39:20,491   adding 'pytim-0.8.0.dist-info/RECORD'
2021-07-13T03:39:20,656   removing build/bdist.linux-armv7l/wheel
2021-07-13T03:39:21,300   Building wheel for pytim (setup.py): finished with status 'done'
2021-07-13T03:39:21,463   Created wheel for pytim: filename=pytim-0.8.0-cp39-cp39-linux_armv7l.whl size=13197135 sha256=e809dbdfc1513190b0b471dabd44ebbb444ca094798928fc50d99021e3de0d3c
2021-07-13T03:39:21,464   Stored in directory: /tmp/pip-ephem-wheel-cache-4wo676vw/wheels/1f/63/3f/ed289bd41c57be853ed1c18d01e7381397578a734f0d04a28b
2021-07-13T03:39:21,480 Successfully built pytim
2021-07-13T03:39:21,882 Removed build tracker: '/tmp/pip-req-tracker-j5ry19i7'