2021-07-12T12:41:31,016 Created temporary directory: /tmp/pip-ephem-wheel-cache-gk0i7eyb 2021-07-12T12:41:31,019 Created temporary directory: /tmp/pip-req-tracker-cajdw6bu 2021-07-12T12:41:31,020 Initialized build tracking at /tmp/pip-req-tracker-cajdw6bu 2021-07-12T12:41:31,021 Created build tracker: /tmp/pip-req-tracker-cajdw6bu 2021-07-12T12:41:31,021 Entered build tracker: /tmp/pip-req-tracker-cajdw6bu 2021-07-12T12:41:31,022 Created temporary directory: /tmp/pip-wheel-gon7sjqs 2021-07-12T12:41:31,059 1 location(s) to search for versions of molmod: 2021-07-12T12:41:31,059 * https://pypi.org/simple/molmod/ 2021-07-12T12:41:31,060 Fetching project page and analyzing links: https://pypi.org/simple/molmod/ 2021-07-12T12:41:31,061 Getting page https://pypi.org/simple/molmod/ 2021-07-12T12:41:31,063 Found index url https://pypi.org/simple 2021-07-12T12:41:31,182 Found link https://files.pythonhosted.org/packages/d8/b1/d7cf3645e70ddf22e3c93225a0f963debc4be6276148cbaed46e973d2064/molmod-1.2.1.tar.gz#sha256=9fc0372f99b2e00fe6fc4ae9954d31b19a767c40c97423c6ee4ada76f3dd9843 (from https://pypi.org/simple/molmod/), version: 1.2.1 2021-07-12T12:41:31,182 Found link https://files.pythonhosted.org/packages/03/2d/4457e38b0e8245af76b37000ccee228d12b029023b0711954bc495494fd0/molmod-1.3.0.tar.gz#sha256=1ed88d05ced28f998b1644f1d400853d30faba8eb06ebb818b22704f2f3cad80 (from https://pypi.org/simple/molmod/), version: 1.3.0 2021-07-12T12:41:31,183 Found link https://files.pythonhosted.org/packages/2c/3d/dd9c32cebc2ee7f29a16a778d775ce074c7c1c7b083f83b0dd63e350927e/molmod-1.3.1.tar.gz#sha256=eee1b0035ef238a9086f71c07bc27563f1481c99ecb172118f41c1f024d6c9fb (from https://pypi.org/simple/molmod/), version: 1.3.1 2021-07-12T12:41:31,183 Found link https://files.pythonhosted.org/packages/79/fd/9f4282bf37b3ee38242dc4c6883b0923d450331f491ab5942702b791e84a/molmod-1.3.2.tar.gz#sha256=0af0b797cf628458e1f5c0334cf7f7f1c2ee6a3edbba87ca0fbde39e9b444ec7 (from https://pypi.org/simple/molmod/), version: 1.3.2 2021-07-12T12:41:31,184 Found link https://files.pythonhosted.org/packages/8c/b1/a243fe8d060c2ccb643e70504b0a727fe4a3420b2c790e3718865b6ffc8c/molmod-1.3.3.tar.gz#sha256=3bcdfb73faf4c3f180e68f7c8efe7fdd58e0e8ce8e8f3883bc4dfb5a260f63db (from https://pypi.org/simple/molmod/), version: 1.3.3 2021-07-12T12:41:31,185 Found link https://files.pythonhosted.org/packages/0d/d2/5df39f43e2f91f5a13376ef2c34aa30de3fd9be11fb6e9e5c18a9e15c9f8/molmod-1.3.4.tar.gz#sha256=c39fc75fa76a6c1c14b0fb41e7e76802b3dad5d695ae62b2afa0ebcc36b37cb4 (from https://pypi.org/simple/molmod/), version: 1.3.4 2021-07-12T12:41:31,185 Found link https://files.pythonhosted.org/packages/5f/dc/39d3239d5d8d54bfc49378235b7c20f010ba98f3c4552b841617884d3646/molmod-1.3.5.tar.gz#sha256=5360f2afab0c09eb6a1124b4deec63966f8aaa5c90176890a9980e242fa4c53c (from https://pypi.org/simple/molmod/), version: 1.3.5 2021-07-12T12:41:31,186 Found link https://files.pythonhosted.org/packages/da/f3/41c1c6830eae57a2b96b0d0d9d1853de31119ab7db44136ef69d3690f21a/molmod-1.4.0.tar.gz#sha256=4dbb214faa90e7e08c9dc54d9b5595c2aa6e2a946c1dcf7defb13e1f9b6fe914 (from https://pypi.org/simple/molmod/), version: 1.4.0 2021-07-12T12:41:31,186 Found link https://files.pythonhosted.org/packages/03/bc/ca927944923a5de71f19c2390ab0b5f99f5e4723a1661c5917ab2cfe9919/molmod-1.4.1.tar.gz#sha256=51992a9e46259293f1851d50a77ddef6ed4d4522826b5452eebd2166f0ffd1d7 (from https://pypi.org/simple/molmod/), version: 1.4.1 2021-07-12T12:41:31,187 Found link https://files.pythonhosted.org/packages/8a/b8/0edf642e6a0bcb411523f5a25f87f1db08b590a073cb3e21dc332407a663/molmod-1.4.2.tar.gz#sha256=c5a533ccdd13e7ffa7ad7c1dec6d49e6279b27b79584a7bd27056b16711e74cd (from https://pypi.org/simple/molmod/), version: 1.4.2 2021-07-12T12:41:31,187 Found link https://files.pythonhosted.org/packages/0b/85/bb75ec4376a612f3e5300712c5e1abab63894ec1bbf7be249a42a90b2c66/molmod-1.4.3.tar.gz#sha256=a93e694e07e36fe5881dc19b8d004c5c4e0514bc5b1240de04497c6aaa99ecf6 (from https://pypi.org/simple/molmod/), version: 1.4.3 2021-07-12T12:41:31,188 Found link https://files.pythonhosted.org/packages/89/80/6a23f730196ed3ffb478dc3f9ea047913c99091d301cc82f4820ecee095d/molmod-1.4.4.tar.gz#sha256=ca0e461fe42fc8b7e0b481cda33aac247d86b5fb817b5076e20abc90dd577797 (from https://pypi.org/simple/molmod/), version: 1.4.4 2021-07-12T12:41:31,188 Found link https://files.pythonhosted.org/packages/98/08/f84c490fe1a2d0e3ff55dddd1079eeb77b2742ed3c8ad49b392444031d2f/molmod-1.4.5.tar.gz#sha256=e94520945c066c26494f20bbf7f85711458acc56b22da7b0da9e48b5b1a2ec35 (from https://pypi.org/simple/molmod/), version: 1.4.5 2021-07-12T12:41:31,189 Found link https://files.pythonhosted.org/packages/e0/ce/a5df4a468f492baf8cce68318fd74eac947ff7f0947afc5bb14ac85fdccb/molmod-1.4.6.tar.gz#sha256=3147eec3a57da164415359188a02385b9285486e70e98f9fc8e2d03037a8ffe3 (from https://pypi.org/simple/molmod/), version: 1.4.6 2021-07-12T12:41:31,190 Found link https://files.pythonhosted.org/packages/31/e6/4d8fe5e1fdf2077fdcee631d56aaaf8efaa331d823c4edc870fb30d701d8/molmod-1.4.7.tar.gz#sha256=bd52ddbfafd8ce88351ba8473580dee760cd1df25f90b75396fc75815db18e66 (from https://pypi.org/simple/molmod/), version: 1.4.7 2021-07-12T12:41:31,190 Found link https://files.pythonhosted.org/packages/23/77/814f9302b6df72ef3aa6944edd8b9b0f5e983aed07027828a4e0666c4ef3/molmod-1.4.8.tar.gz#sha256=08cc526080aee04659ff5d08f8d26ab6973afef62becb9ae21cb11bb5b632177 (from https://pypi.org/simple/molmod/), version: 1.4.8 2021-07-12T12:41:31,191 Skipping link: not a file: https://pypi.org/simple/molmod/ 2021-07-12T12:41:31,220 Given no hashes to check 1 links for project 'molmod': discarding no candidates 2021-07-12T12:41:31,247 Collecting molmod==1.3.3 2021-07-12T12:41:31,249 Created temporary directory: /tmp/pip-unpack-2bx3lt57 2021-07-12T12:41:32,247 Downloading molmod-1.3.3.tar.gz (1.7 MB) 2021-07-12T12:41:33,459 Added molmod==1.3.3 from https://files.pythonhosted.org/packages/8c/b1/a243fe8d060c2ccb643e70504b0a727fe4a3420b2c790e3718865b6ffc8c/molmod-1.3.3.tar.gz#sha256=3bcdfb73faf4c3f180e68f7c8efe7fdd58e0e8ce8e8f3883bc4dfb5a260f63db to build tracker '/tmp/pip-req-tracker-cajdw6bu' 2021-07-12T12:41:33,461 Running setup.py (path:/tmp/pip-wheel-gon7sjqs/molmod_d41d2b770b8f45a8843c3270f22ff4f2/setup.py) egg_info for package molmod 2021-07-12T12:41:33,462 Created temporary directory: /tmp/pip-pip-egg-info-hmryejsz 2021-07-12T12:41:33,462 Running command python setup.py egg_info 2021-07-12T12:41:34,953 fatal: not a git repository (or any of the parent directories): .git 2021-07-12T12:41:35,179 running egg_info 2021-07-12T12:41:35,182 creating /tmp/pip-pip-egg-info-hmryejsz/molmod.egg-info 2021-07-12T12:41:35,183 writing /tmp/pip-pip-egg-info-hmryejsz/molmod.egg-info/PKG-INFO 2021-07-12T12:41:35,185 writing dependency_links to /tmp/pip-pip-egg-info-hmryejsz/molmod.egg-info/dependency_links.txt 2021-07-12T12:41:35,187 writing requirements to /tmp/pip-pip-egg-info-hmryejsz/molmod.egg-info/requires.txt 2021-07-12T12:41:35,188 writing top-level names to /tmp/pip-pip-egg-info-hmryejsz/molmod.egg-info/top_level.txt 2021-07-12T12:41:35,190 writing manifest file '/tmp/pip-pip-egg-info-hmryejsz/molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:35,389 reading manifest file '/tmp/pip-pip-egg-info-hmryejsz/molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:35,391 reading manifest template 'MANIFEST.in' 2021-07-12T12:41:35,809 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2021-07-12T12:41:35,879 adding license file 'LICENSE.txt' 2021-07-12T12:41:35,891 writing manifest file '/tmp/pip-pip-egg-info-hmryejsz/molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:36,030 Source in /tmp/pip-wheel-gon7sjqs/molmod_d41d2b770b8f45a8843c3270f22ff4f2 has version 1.3.3, which satisfies requirement molmod==1.3.3 from https://files.pythonhosted.org/packages/8c/b1/a243fe8d060c2ccb643e70504b0a727fe4a3420b2c790e3718865b6ffc8c/molmod-1.3.3.tar.gz#sha256=3bcdfb73faf4c3f180e68f7c8efe7fdd58e0e8ce8e8f3883bc4dfb5a260f63db 2021-07-12T12:41:36,031 Removed molmod==1.3.3 from https://files.pythonhosted.org/packages/8c/b1/a243fe8d060c2ccb643e70504b0a727fe4a3420b2c790e3718865b6ffc8c/molmod-1.3.3.tar.gz#sha256=3bcdfb73faf4c3f180e68f7c8efe7fdd58e0e8ce8e8f3883bc4dfb5a260f63db from build tracker '/tmp/pip-req-tracker-cajdw6bu' 2021-07-12T12:41:36,038 Created temporary directory: /tmp/pip-unpack-0uh71p6j 2021-07-12T12:41:36,039 Building wheels for collected packages: molmod 2021-07-12T12:41:36,045 Created temporary directory: /tmp/pip-wheel-c1eqgrpn 2021-07-12T12:41:36,046 Building wheel for molmod (setup.py): started 2021-07-12T12:41:36,046 Destination directory: /tmp/pip-wheel-c1eqgrpn 2021-07-12T12:41:36,047 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-gon7sjqs/molmod_d41d2b770b8f45a8843c3270f22ff4f2/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-gon7sjqs/molmod_d41d2b770b8f45a8843c3270f22ff4f2/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-c1eqgrpn 2021-07-12T12:41:37,498 fatal: not a git repository (or any of the parent directories): .git 2021-07-12T12:41:37,735 running bdist_wheel 2021-07-12T12:41:37,740 running build 2021-07-12T12:41:37,741 running build_py 2021-07-12T12:41:37,881 creating build 2021-07-12T12:41:37,882 creating build/lib.linux-armv7l-3.9 2021-07-12T12:41:37,882 creating build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,883 copying molmod/toyff.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,886 copying molmod/minimizer.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,890 copying molmod/clusters.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,892 copying molmod/similarity.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,894 copying molmod/unit_cells.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,897 copying molmod/log.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,900 copying molmod/zmatrix.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,903 copying molmod/binning.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,906 copying molmod/molecular_graphs.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,910 copying molmod/__init__.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,912 copying molmod/bonds.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,914 copying molmod/symmetry.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,916 copying molmod/graphs.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,921 copying molmod/version.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,922 copying molmod/vectors.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,925 copying molmod/periodic.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,927 copying molmod/pairff.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,930 copying molmod/utils.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,933 copying molmod/molecules.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,936 copying molmod/quaternions.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,937 copying molmod/transformations.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,940 copying molmod/randomize.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,943 copying molmod/ic.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,946 copying molmod/isotopes.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,948 copying molmod/constants.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,950 copying molmod/units.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,955 creating build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,956 copying molmod/test/test_minimizer.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,958 copying molmod/test/test_binning.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,961 copying molmod/test/test_molecules.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,964 copying molmod/test/test_randomize.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,966 copying molmod/test/test_vectors.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,968 copying molmod/test/test_transformations.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,971 copying molmod/test/__init__.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,973 copying molmod/test/test_log.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,975 copying molmod/test/test_ic.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,978 copying molmod/test/test_clusters.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,980 copying molmod/test/test_units.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,982 copying molmod/test/test_similarity.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,984 copying molmod/test/test_quaternions.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,986 copying molmod/test/common.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,988 copying molmod/test/test_zmatrix.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,990 copying molmod/test/test_pairff.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,993 copying molmod/test/test_utils.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,996 copying molmod/test/test_toyff.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,998 copying molmod/test/test_examples.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:38,001 copying molmod/test/test_symmetry.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:38,003 copying molmod/test/test_unit_cells.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:38,006 copying molmod/test/test_molecular_graphs.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:38,010 copying molmod/test/test_data.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:38,012 copying molmod/test/test_graphs.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:38,017 creating build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,018 copying molmod/io/cpmd.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,021 copying molmod/io/dlpoly.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,023 copying molmod/io/cml.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,026 copying molmod/io/cube.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,029 copying molmod/io/xyz.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,032 copying molmod/io/lammps.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,034 copying molmod/io/gamess.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,037 copying molmod/io/__init__.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,039 copying molmod/io/gromacs.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,041 copying molmod/io/number_state.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,044 copying molmod/io/common.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,046 copying molmod/io/atrj.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,049 copying molmod/io/psf.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,052 copying molmod/io/cp2k.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,054 copying molmod/io/pdb.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,057 copying molmod/io/chk.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,060 copying molmod/io/crystal.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,063 copying molmod/io/sdf.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,065 copying molmod/io/fchk.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:38,069 creating build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,070 copying molmod/io/test/test_sdf.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,073 copying molmod/io/test/test_dlpoly.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,075 copying molmod/io/test/test_gromacs.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,077 copying molmod/io/test/test_number_state.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,079 copying molmod/io/test/test_cml.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,081 copying molmod/io/test/__init__.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,083 copying molmod/io/test/test_cpmd.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,085 copying molmod/io/test/test_crystal.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,087 copying molmod/io/test/test_cube.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,090 copying molmod/io/test/test_lammps.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,092 copying molmod/io/test/test_fchk.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,094 copying molmod/io/test/test_xyz.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,097 copying molmod/io/test/test_atrj.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,099 copying molmod/io/test/test_gamess.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,101 copying molmod/io/test/test_pdb.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,103 copying molmod/io/test/test_cp2k.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,106 copying molmod/io/test/test_psf.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:38,108 running egg_info 2021-07-12T12:41:38,125 writing molmod.egg-info/PKG-INFO 2021-07-12T12:41:38,127 writing dependency_links to molmod.egg-info/dependency_links.txt 2021-07-12T12:41:38,129 writing requirements to molmod.egg-info/requires.txt 2021-07-12T12:41:38,131 writing top-level names to molmod.egg-info/top_level.txt 2021-07-12T12:41:38,180 reading manifest file 'molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:38,190 reading manifest template 'MANIFEST.in' 2021-07-12T12:41:38,596 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2021-07-12T12:41:38,663 adding license file 'LICENSE.txt' 2021-07-12T12:41:38,679 writing manifest file 'molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:38,696 copying molmod/common.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,699 copying molmod/common.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,701 copying molmod/ext.pyx -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,704 copying molmod/ff.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,706 copying molmod/ff.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,708 copying molmod/ff.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,710 copying molmod/graphs.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,713 copying molmod/graphs.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,715 copying molmod/graphs.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,717 copying molmod/molecules.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,720 copying molmod/molecules.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,722 copying molmod/molecules.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,725 copying molmod/similarity.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,727 copying molmod/similarity.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,729 copying molmod/similarity.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,732 copying molmod/unit_cells.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,735 copying molmod/unit_cells.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,738 copying molmod/unit_cells.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:38,740 creating build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:38,741 copying molmod/data/bonds.csv -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:38,744 copying molmod/data/bonds.ods -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:38,748 copying molmod/data/mass.mas03 -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:38,764 copying molmod/data/nubtab03.asc -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:38,784 copying molmod/data/periodic.csv -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:38,787 copying molmod/data/periodic.ods -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:38,791 copying molmod/data/toyff_angles.txt -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:38,795 creating build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,796 copying molmod/data/test/1LJL_Cys10.cml -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,800 copying molmod/data/test/1TOH.b3lyp.fchk -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,817 copying molmod/data/test/1TOH.b3lyp.trim.fchk -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,820 copying molmod/data/test/5ringOH.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,822 copying molmod/data/test/CID_22898828.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,824 copying molmod/data/test/PCGamess_PUNCH -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,847 copying molmod/data/test/SID_31646545.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,849 copying molmod/data/test/SID_31646548.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,852 copying molmod/data/test/SID_40363570.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,854 copying molmod/data/test/SID_40363571.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,857 copying molmod/data/test/SID_41893278.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,859 copying molmod/data/test/SID_41893280.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,862 copying molmod/data/test/SID_54258192.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,864 copying molmod/data/test/SID_55127927.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,867 copying molmod/data/test/SID_55488598.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,870 copying molmod/data/test/SID_56274343.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,872 copying molmod/data/test/TRAJECTORY_H2_CPMD -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,875 copying molmod/data/test/alanine.cube -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,878 copying molmod/data/test/argon.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,881 copying molmod/data/test/bartek.atrj -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,892 copying molmod/data/test/benzene.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,895 copying molmod/data/test/butane.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,897 copying molmod/data/test/caplayer.cml -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,900 copying molmod/data/test/crystal_api.out -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,915 copying molmod/data/test/cyclopentane.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,918 copying molmod/data/test/dinitrogen.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,920 copying molmod/data/test/dlpoly_HISTORY -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,922 copying molmod/data/test/dlpoly_HISTORY_an2 -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,925 copying molmod/data/test/dlpoly_OUTPUT -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,929 copying molmod/data/test/dopamine.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,931 copying molmod/data/test/ethane.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,934 copying molmod/data/test/ethene.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,936 copying molmod/data/test/ethene_ethyl_trans.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,939 copying molmod/data/test/example.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,942 copying molmod/data/test/formol.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,945 copying molmod/data/test/funny.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,947 copying molmod/data/test/h3zrosihohosioh3.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,950 copying molmod/data/test/il2.pdb -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,957 copying molmod/data/test/lammps_dump.txt -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,960 copying molmod/data/test/lau.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,963 copying molmod/data/test/octane.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,966 copying molmod/data/test/oh3siozroh3.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,968 copying molmod/data/test/opt_5ring10T.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,971 copying molmod/data/test/opt_5ring12T.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,974 copying molmod/data/test/opt_6_6ring.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,976 copying molmod/data/test/opt_6ring.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,980 copying molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,982 copying molmod/data/test/pentapeptide.psf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,985 copying molmod/data/test/precursor.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,989 copying molmod/data/test/probes.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,991 copying molmod/data/test/tea.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,994 copying molmod/data/test/tetra.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,996 copying molmod/data/test/thf.psf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,003 copying molmod/data/test/thf.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,007 copying molmod/data/test/thf_64.cell -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,010 copying molmod/data/test/thf_single.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,013 copying molmod/data/test/tpa.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,015 copying molmod/data/test/water.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,018 copying molmod/data/test/water2.gro -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,021 copying molmod/data/test/water_md.inp -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,023 copying molmod/data/test/zr4o8-3.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:39,026 creating build/lib.linux-armv7l-3.9/molmod/examples 2021-07-12T12:41:39,026 creating build/lib.linux-armv7l-3.9/molmod/examples/000_units 2021-07-12T12:41:39,027 copying molmod/examples/000_units/a_reaction.py -> build/lib.linux-armv7l-3.9/molmod/examples/000_units 2021-07-12T12:41:39,030 copying molmod/examples/000_units/b_chbond.py -> build/lib.linux-armv7l-3.9/molmod/examples/000_units 2021-07-12T12:41:39,033 copying molmod/examples/000_units/c_h2rot.py -> build/lib.linux-armv7l-3.9/molmod/examples/000_units 2021-07-12T12:41:39,035 creating build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:39,036 copying molmod/examples/001_molecules/a_convert.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:39,039 copying molmod/examples/001_molecules/b_com.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:39,042 copying molmod/examples/001_molecules/c_carbon.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:39,044 copying molmod/examples/001_molecules/d_size.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:39,047 copying molmod/examples/001_molecules/e_shape.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:39,049 copying molmod/examples/001_molecules/ibuprofen.sdf -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:39,052 creating build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:39,053 copying molmod/examples/002_graphs/a_graphs.py -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:39,056 copying molmod/examples/002_graphs/b_neighbors.py -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:39,059 copying molmod/examples/002_graphs/c_distances.py -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:39,061 copying molmod/examples/002_graphs/caffeine.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:39,064 copying molmod/examples/002_graphs/d_symmetries.py -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:39,066 copying molmod/examples/002_graphs/ethanol.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:39,069 creating build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:39,070 copying molmod/examples/003_internal_coordinates/a_bond_length.py -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:39,072 copying molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:39,075 copying molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:39,078 copying molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:39,081 copying molmod/examples/003_internal_coordinates/dopamine.fchk -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:39,085 copying molmod/examples/003_internal_coordinates/dopamine.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:39,088 copying molmod/examples/003_internal_coordinates/propane.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:39,091 creating build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:39,091 copying molmod/examples/004_patterns/a_propane_types.py -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:39,094 copying molmod/examples/004_patterns/b_dopamine_types.py -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:39,097 copying molmod/examples/004_patterns/dopamine.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:39,100 copying molmod/examples/004_patterns/mfi_fragment.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:39,103 copying molmod/examples/004_patterns/propane.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:39,114 running build_ext 2021-07-12T12:41:39,120 cythoning molmod/ext.pyx to molmod/ext.c 2021-07-12T12:41:39,794 /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-gon7sjqs/molmod_d41d2b770b8f45a8843c3270f22ff4f2/molmod/ext.pyx 2021-07-12T12:41:39,794 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T12:41:47,732 building 'molmod.ext' extension 2021-07-12T12:41:47,733 creating build/temp.linux-armv7l-3.9 2021-07-12T12:41:47,733 creating build/temp.linux-armv7l-3.9/molmod 2021-07-12T12:41:47,734 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 molmod/common.c -o build/temp.linux-armv7l-3.9/molmod/common.o 2021-07-12T12:41:48,030 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 molmod/ext.c -o build/temp.linux-armv7l-3.9/molmod/ext.o 2021-07-12T12:41:48,470 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-12T12:41:48,470 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-12T12:41:48,470 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-12T12:41:48,470 from molmod/ext.c:612: 2021-07-12T12:41:48,471 /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] 2021-07-12T12:41:48,471 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-12T12:41:48,471 | ^~~~~~~ 2021-07-12T12:41:48,559 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_ff_dm_quad’: 2021-07-12T12:41:48,561 molmod/ext.c:2923:40: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,561 2923 | __pyx_t_3 = (((__pyx_v_dm0.shape[0]) != __pyx_v_natom) != 0); 2021-07-12T12:41:48,562 | ^~ 2021-07-12T12:41:48,563 molmod/ext.c:2929:40: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,563 2929 | __pyx_t_3 = (((__pyx_v_dm0.shape[1]) != __pyx_v_natom) != 0); 2021-07-12T12:41:48,563 | ^~ 2021-07-12T12:41:48,565 molmod/ext.c:2963:40: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,565 2963 | __pyx_t_3 = (((__pyx_v_dmk.shape[0]) != __pyx_v_natom) != 0); 2021-07-12T12:41:48,566 | ^~ 2021-07-12T12:41:48,567 molmod/ext.c:2969:40: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,567 2969 | __pyx_t_3 = (((__pyx_v_dmk.shape[1]) != __pyx_v_natom) != 0); 2021-07-12T12:41:48,568 | ^~ 2021-07-12T12:41:48,615 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_2ff_dm_reci’: 2021-07-12T12:41:48,618 molmod/ext.c:3679:42: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,618 3679 | __pyx_t_1 = (((__pyx_v_radii.shape[0]) != __pyx_v_natom) != 0); 2021-07-12T12:41:48,618 | ^~ 2021-07-12T12:41:48,620 molmod/ext.c:3711:40: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,621 3711 | __pyx_t_3 = (((__pyx_v_dm0.shape[0]) != __pyx_v_natom) != 0); 2021-07-12T12:41:48,621 | ^~ 2021-07-12T12:41:48,623 molmod/ext.c:3717:40: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,623 3717 | __pyx_t_3 = (((__pyx_v_dm0.shape[1]) != __pyx_v_natom) != 0); 2021-07-12T12:41:48,623 | ^~ 2021-07-12T12:41:48,682 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_4ff_bond_quad’: 2021-07-12T12:41:48,685 molmod/ext.c:4583:44: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,685 4583 | __pyx_t_1 = (((__pyx_v_lengths.shape[0]) != __pyx_v_npair) != 0); 2021-07-12T12:41:48,685 | ^~ 2021-07-12T12:41:48,747 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_6ff_bond_hyper’: 2021-07-12T12:41:48,751 molmod/ext.c:5327:44: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,751 5327 | __pyx_t_1 = (((__pyx_v_lengths.shape[0]) != __pyx_v_npair) != 0); 2021-07-12T12:41:48,751 | ^~ 2021-07-12T12:41:48,816 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_8graphs_floyd_warshall’: 2021-07-12T12:41:48,820 molmod/ext.c:5858:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,820 5858 | __pyx_t_1 = (((__pyx_v_dm.shape[1]) != __pyx_v_nvertex) != 0); 2021-07-12T12:41:48,820 | ^~ 2021-07-12T12:41:48,898 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_12similarity_table_labels’: 2021-07-12T12:41:48,902 molmod/ext.c:6700:39: warning: passing argument 2 of ‘similarity_table_labels’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-12T12:41:48,902 6700 | similarity_table_labels(__pyx_v_n, (&(*((long const *) ( /* dim=0 */ ((char *) (((long const *) __pyx_v_labels.data) + __pyx_t_6)) )))), (&(*__Pyx_BufPtrStrided2d(long *, __pyx_pybuffernd_labels_table.rcbuffer->pybuffer.buf, __pyx_t_8, __pyx_pybuffernd_labels_table.diminfo[0].strides, __pyx_t_9, __pyx_pybuffernd_labels_table.diminfo[1].strides)))); 2021-07-12T12:41:48,903 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T12:41:48,903 In file included from molmod/ext.c:623: 2021-07-12T12:41:48,903 molmod/similarity.h:30:46: note: expected ‘long int *’ but argument is of type ‘const long int *’ 2021-07-12T12:41:48,903 30 | void similarity_table_labels(size_t n, long *labels, long* labels_table); 2021-07-12T12:41:48,904 | ~~~~~~^~~~~~ 2021-07-12T12:41:48,905 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_14similarity_table_distances’: 2021-07-12T12:41:48,909 molmod/ext.c:6831:52: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,909 6831 | __pyx_t_1 = (((__pyx_v_distance_matrix.shape[1]) != __pyx_v_n) != 0); 2021-07-12T12:41:48,910 | ^~ 2021-07-12T12:41:48,929 molmod/ext.c:6929:42: warning: passing argument 2 of ‘similarity_table_distances’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-12T12:41:48,929 6929 | similarity_table_distances(__pyx_v_n, (&(*((double const *) ( /* dim=1 */ ((char *) (((double const *) ( /* dim=0 */ (__pyx_v_distance_matrix.data + __pyx_t_7 * __pyx_v_distance_matrix.strides[0]) )) + __pyx_t_8)) )))), (&(*__Pyx_BufPtrStrided1d(double *, __pyx_pybuffernd_distances_table.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_distances_table.diminfo[0].strides)))); 2021-07-12T12:41:48,929 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T12:41:48,929 In file included from molmod/ext.c:623: 2021-07-12T12:41:48,930 molmod/similarity.h:31:51: note: expected ‘double *’ but argument is of type ‘const double *’ 2021-07-12T12:41:48,930 31 | void similarity_table_distances(size_t n, double *distance_matrix, double *distances_table); 2021-07-12T12:41:48,930 | ~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-12T12:41:48,938 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_16similarity_measure’: 2021-07-12T12:41:48,942 molmod/ext.c:7185:47: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,943 7185 | __pyx_t_1 = (((__pyx_v_distances1.shape[0]) != __pyx_v_n1) != 0); 2021-07-12T12:41:48,943 | ^~ 2021-07-12T12:41:48,948 molmod/ext.c:7249:47: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-12T12:41:48,949 7249 | __pyx_t_1 = (((__pyx_v_distances2.shape[0]) != __pyx_v_n2) != 0); 2021-07-12T12:41:48,949 | ^~ 2021-07-12T12:42:07,237 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 molmod/ff.c -o build/temp.linux-armv7l-3.9/molmod/ff.o 2021-07-12T12:42:07,632 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 molmod/graphs.c -o build/temp.linux-armv7l-3.9/molmod/graphs.o 2021-07-12T12:42:07,784 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 molmod/molecules.c -o build/temp.linux-armv7l-3.9/molmod/molecules.o 2021-07-12T12:42:07,947 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 molmod/similarity.c -o build/temp.linux-armv7l-3.9/molmod/similarity.o 2021-07-12T12:42:08,196 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 molmod/unit_cells.c -o build/temp.linux-armv7l-3.9/molmod/unit_cells.o 2021-07-12T12:42:08,565 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/molmod/common.o build/temp.linux-armv7l-3.9/molmod/ext.o build/temp.linux-armv7l-3.9/molmod/ff.o build/temp.linux-armv7l-3.9/molmod/graphs.o build/temp.linux-armv7l-3.9/molmod/molecules.o build/temp.linux-armv7l-3.9/molmod/similarity.o build/temp.linux-armv7l-3.9/molmod/unit_cells.o -o build/lib.linux-armv7l-3.9/molmod/ext.cpython-39-arm-linux-gnueabihf.so 2021-07-12T12:42:08,788 installing to build/bdist.linux-armv7l/wheel 2021-07-12T12:42:08,788 running install 2021-07-12T12:42:08,790 running install_lib 2021-07-12T12:42:08,800 creating build/bdist.linux-armv7l 2021-07-12T12:42:08,800 creating build/bdist.linux-armv7l/wheel 2021-07-12T12:42:08,803 creating build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,804 copying build/lib.linux-armv7l-3.9/molmod/toyff.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,807 copying build/lib.linux-armv7l-3.9/molmod/ext.pyx -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,809 copying build/lib.linux-armv7l-3.9/molmod/graphs.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,811 copying build/lib.linux-armv7l-3.9/molmod/minimizer.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,815 copying build/lib.linux-armv7l-3.9/molmod/clusters.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,818 copying build/lib.linux-armv7l-3.9/molmod/similarity.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,820 copying build/lib.linux-armv7l-3.9/molmod/unit_cells.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,823 copying build/lib.linux-armv7l-3.9/molmod/common.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,825 copying build/lib.linux-armv7l-3.9/molmod/log.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,828 copying build/lib.linux-armv7l-3.9/molmod/zmatrix.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,830 copying build/lib.linux-armv7l-3.9/molmod/binning.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,834 creating build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,835 copying build/lib.linux-armv7l-3.9/molmod/io/cpmd.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,837 copying build/lib.linux-armv7l-3.9/molmod/io/dlpoly.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,840 copying build/lib.linux-armv7l-3.9/molmod/io/cml.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,842 copying build/lib.linux-armv7l-3.9/molmod/io/cube.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,844 copying build/lib.linux-armv7l-3.9/molmod/io/xyz.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,847 copying build/lib.linux-armv7l-3.9/molmod/io/lammps.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,849 copying build/lib.linux-armv7l-3.9/molmod/io/gamess.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,852 copying build/lib.linux-armv7l-3.9/molmod/io/__init__.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,854 copying build/lib.linux-armv7l-3.9/molmod/io/gromacs.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,856 copying build/lib.linux-armv7l-3.9/molmod/io/number_state.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,858 copying build/lib.linux-armv7l-3.9/molmod/io/common.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,860 copying build/lib.linux-armv7l-3.9/molmod/io/atrj.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,863 creating build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,864 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_sdf.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,867 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_dlpoly.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,869 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_gromacs.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,871 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_number_state.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,873 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_cml.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,875 copying build/lib.linux-armv7l-3.9/molmod/io/test/__init__.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,877 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_cpmd.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,879 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_crystal.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,882 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_cube.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,884 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_lammps.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,886 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_fchk.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,888 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_xyz.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,891 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_atrj.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,893 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_gamess.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,895 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_pdb.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,897 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_cp2k.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,900 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_psf.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:08,902 copying build/lib.linux-armv7l-3.9/molmod/io/psf.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,904 copying build/lib.linux-armv7l-3.9/molmod/io/cp2k.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,907 copying build/lib.linux-armv7l-3.9/molmod/io/pdb.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,910 copying build/lib.linux-armv7l-3.9/molmod/io/chk.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,912 copying build/lib.linux-armv7l-3.9/molmod/io/crystal.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,914 copying build/lib.linux-armv7l-3.9/molmod/io/sdf.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,917 copying build/lib.linux-armv7l-3.9/molmod/io/fchk.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:08,919 copying build/lib.linux-armv7l-3.9/molmod/ext.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,943 copying build/lib.linux-armv7l-3.9/molmod/molecular_graphs.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,946 copying build/lib.linux-armv7l-3.9/molmod/molecules.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,948 copying build/lib.linux-armv7l-3.9/molmod/__init__.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,950 copying build/lib.linux-armv7l-3.9/molmod/bonds.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:08,953 creating build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:08,954 copying build/lib.linux-armv7l-3.9/molmod/data/toyff_angles.txt -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:08,958 copying build/lib.linux-armv7l-3.9/molmod/data/nubtab03.asc -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:08,972 copying build/lib.linux-armv7l-3.9/molmod/data/mass.mas03 -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:08,994 copying build/lib.linux-armv7l-3.9/molmod/data/bonds.ods -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:08,999 creating build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,000 copying build/lib.linux-armv7l-3.9/molmod/data/test/bartek.atrj -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,010 copying build/lib.linux-armv7l-3.9/molmod/data/test/lau.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,012 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_31646548.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,014 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_41893278.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,016 copying build/lib.linux-armv7l-3.9/molmod/data/test/example.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,018 copying build/lib.linux-armv7l-3.9/molmod/data/test/dlpoly_HISTORY_an2 -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,020 copying build/lib.linux-armv7l-3.9/molmod/data/test/precursor.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,022 copying build/lib.linux-armv7l-3.9/molmod/data/test/TRAJECTORY_H2_CPMD -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,024 copying build/lib.linux-armv7l-3.9/molmod/data/test/butane.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,026 copying build/lib.linux-armv7l-3.9/molmod/data/test/opt_5ring12T.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,028 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_40363571.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,030 copying build/lib.linux-armv7l-3.9/molmod/data/test/opt_6_6ring.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,032 copying build/lib.linux-armv7l-3.9/molmod/data/test/water_md.inp -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,034 copying build/lib.linux-armv7l-3.9/molmod/data/test/CID_22898828.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,036 copying build/lib.linux-armv7l-3.9/molmod/data/test/caplayer.cml -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,038 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_55127927.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,041 copying build/lib.linux-armv7l-3.9/molmod/data/test/1LJL_Cys10.cml -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,044 copying build/lib.linux-armv7l-3.9/molmod/data/test/lammps_dump.txt -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,046 copying build/lib.linux-armv7l-3.9/molmod/data/test/thf.psf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,053 copying build/lib.linux-armv7l-3.9/molmod/data/test/thf_64.cell -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,055 copying build/lib.linux-armv7l-3.9/molmod/data/test/zr4o8-3.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,057 copying build/lib.linux-armv7l-3.9/molmod/data/test/h3zrosihohosioh3.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,059 copying build/lib.linux-armv7l-3.9/molmod/data/test/alanine.cube -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,062 copying build/lib.linux-armv7l-3.9/molmod/data/test/water.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,064 copying build/lib.linux-armv7l-3.9/molmod/data/test/tea.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,067 copying build/lib.linux-armv7l-3.9/molmod/data/test/ethane.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,069 copying build/lib.linux-armv7l-3.9/molmod/data/test/PCGamess_PUNCH -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,090 copying build/lib.linux-armv7l-3.9/molmod/data/test/funny.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,092 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_40363570.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,095 copying build/lib.linux-armv7l-3.9/molmod/data/test/opt_5ring10T.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,097 copying build/lib.linux-armv7l-3.9/molmod/data/test/tpa.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,100 copying build/lib.linux-armv7l-3.9/molmod/data/test/tetra.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,102 copying build/lib.linux-armv7l-3.9/molmod/data/test/crystal_api.out -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,114 copying build/lib.linux-armv7l-3.9/molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,117 copying build/lib.linux-armv7l-3.9/molmod/data/test/il2.pdb -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,124 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_55488598.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,126 copying build/lib.linux-armv7l-3.9/molmod/data/test/pentapeptide.psf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,129 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_41893280.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,132 copying build/lib.linux-armv7l-3.9/molmod/data/test/dlpoly_OUTPUT -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,137 copying build/lib.linux-armv7l-3.9/molmod/data/test/cyclopentane.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,140 copying build/lib.linux-armv7l-3.9/molmod/data/test/1TOH.b3lyp.fchk -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,157 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_54258192.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,160 copying build/lib.linux-armv7l-3.9/molmod/data/test/5ringOH.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,162 copying build/lib.linux-armv7l-3.9/molmod/data/test/octane.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,165 copying build/lib.linux-armv7l-3.9/molmod/data/test/argon.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,168 copying build/lib.linux-armv7l-3.9/molmod/data/test/dlpoly_HISTORY -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,171 copying build/lib.linux-armv7l-3.9/molmod/data/test/ethene.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,174 copying build/lib.linux-armv7l-3.9/molmod/data/test/formol.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,176 copying build/lib.linux-armv7l-3.9/molmod/data/test/opt_6ring.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,179 copying build/lib.linux-armv7l-3.9/molmod/data/test/ethene_ethyl_trans.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,182 copying build/lib.linux-armv7l-3.9/molmod/data/test/dopamine.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,184 copying build/lib.linux-armv7l-3.9/molmod/data/test/thf_single.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,187 copying build/lib.linux-armv7l-3.9/molmod/data/test/oh3siozroh3.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,190 copying build/lib.linux-armv7l-3.9/molmod/data/test/benzene.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,192 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_31646545.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,195 copying build/lib.linux-armv7l-3.9/molmod/data/test/water2.gro -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,198 copying build/lib.linux-armv7l-3.9/molmod/data/test/dinitrogen.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,201 copying build/lib.linux-armv7l-3.9/molmod/data/test/1TOH.b3lyp.trim.fchk -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,204 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_56274343.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,207 copying build/lib.linux-armv7l-3.9/molmod/data/test/probes.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,209 copying build/lib.linux-armv7l-3.9/molmod/data/test/thf.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:09,213 copying build/lib.linux-armv7l-3.9/molmod/data/periodic.ods -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:09,217 copying build/lib.linux-armv7l-3.9/molmod/data/periodic.csv -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:09,220 copying build/lib.linux-armv7l-3.9/molmod/data/bonds.csv -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:09,223 copying build/lib.linux-armv7l-3.9/molmod/similarity.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,226 copying build/lib.linux-armv7l-3.9/molmod/symmetry.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,229 copying build/lib.linux-armv7l-3.9/molmod/ff.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,231 copying build/lib.linux-armv7l-3.9/molmod/common.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,234 copying build/lib.linux-armv7l-3.9/molmod/graphs.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,239 copying build/lib.linux-armv7l-3.9/molmod/version.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,242 copying build/lib.linux-armv7l-3.9/molmod/ff.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,245 copying build/lib.linux-armv7l-3.9/molmod/unit_cells.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,248 copying build/lib.linux-armv7l-3.9/molmod/graphs.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,250 copying build/lib.linux-armv7l-3.9/molmod/vectors.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,253 copying build/lib.linux-armv7l-3.9/molmod/molecules.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,256 copying build/lib.linux-armv7l-3.9/molmod/periodic.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,259 copying build/lib.linux-armv7l-3.9/molmod/pairff.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,264 creating build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,265 copying build/lib.linux-armv7l-3.9/molmod/test/test_minimizer.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,269 copying build/lib.linux-armv7l-3.9/molmod/test/test_binning.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,272 copying build/lib.linux-armv7l-3.9/molmod/test/test_molecules.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,276 copying build/lib.linux-armv7l-3.9/molmod/test/test_randomize.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,279 copying build/lib.linux-armv7l-3.9/molmod/test/test_vectors.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,281 copying build/lib.linux-armv7l-3.9/molmod/test/test_transformations.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,285 copying build/lib.linux-armv7l-3.9/molmod/test/__init__.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,288 copying build/lib.linux-armv7l-3.9/molmod/test/test_log.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,291 copying build/lib.linux-armv7l-3.9/molmod/test/test_ic.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,294 copying build/lib.linux-armv7l-3.9/molmod/test/test_clusters.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,297 copying build/lib.linux-armv7l-3.9/molmod/test/test_units.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,300 copying build/lib.linux-armv7l-3.9/molmod/test/test_similarity.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,302 copying build/lib.linux-armv7l-3.9/molmod/test/test_quaternions.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,305 copying build/lib.linux-armv7l-3.9/molmod/test/common.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,308 copying build/lib.linux-armv7l-3.9/molmod/test/test_zmatrix.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,311 copying build/lib.linux-armv7l-3.9/molmod/test/test_pairff.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,314 copying build/lib.linux-armv7l-3.9/molmod/test/test_utils.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,317 copying build/lib.linux-armv7l-3.9/molmod/test/test_toyff.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,321 copying build/lib.linux-armv7l-3.9/molmod/test/test_examples.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,324 copying build/lib.linux-armv7l-3.9/molmod/test/test_symmetry.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,327 copying build/lib.linux-armv7l-3.9/molmod/test/test_unit_cells.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,330 copying build/lib.linux-armv7l-3.9/molmod/test/test_molecular_graphs.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,334 copying build/lib.linux-armv7l-3.9/molmod/test/test_data.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,336 copying build/lib.linux-armv7l-3.9/molmod/test/test_graphs.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:09,341 copying build/lib.linux-armv7l-3.9/molmod/unit_cells.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,344 copying build/lib.linux-armv7l-3.9/molmod/utils.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,347 copying build/lib.linux-armv7l-3.9/molmod/molecules.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,351 copying build/lib.linux-armv7l-3.9/molmod/ff.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,354 copying build/lib.linux-armv7l-3.9/molmod/unit_cells.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,357 copying build/lib.linux-armv7l-3.9/molmod/quaternions.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,360 copying build/lib.linux-armv7l-3.9/molmod/transformations.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,363 copying build/lib.linux-armv7l-3.9/molmod/similarity.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,366 copying build/lib.linux-armv7l-3.9/molmod/randomize.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,369 copying build/lib.linux-armv7l-3.9/molmod/ic.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,373 copying build/lib.linux-armv7l-3.9/molmod/graphs.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,376 copying build/lib.linux-armv7l-3.9/molmod/similarity.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,379 copying build/lib.linux-armv7l-3.9/molmod/molecules.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,381 copying build/lib.linux-armv7l-3.9/molmod/isotopes.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,385 creating build/bdist.linux-armv7l/wheel/molmod/examples 2021-07-12T12:42:09,388 creating build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:09,389 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/caffeine.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:09,392 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/a_graphs.py -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:09,395 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/b_neighbors.py -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:09,398 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/d_symmetries.py -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:09,400 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/ethanol.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:09,403 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/c_distances.py -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:09,406 creating build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:09,408 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:09,411 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:09,414 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/propane.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:09,416 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:09,419 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/dopamine.fchk -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:09,424 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/a_bond_length.py -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:09,427 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/dopamine.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:09,430 creating build/bdist.linux-armv7l/wheel/molmod/examples/000_units 2021-07-12T12:42:09,431 copying build/lib.linux-armv7l-3.9/molmod/examples/000_units/b_chbond.py -> build/bdist.linux-armv7l/wheel/molmod/examples/000_units 2021-07-12T12:42:09,434 copying build/lib.linux-armv7l-3.9/molmod/examples/000_units/c_h2rot.py -> build/bdist.linux-armv7l/wheel/molmod/examples/000_units 2021-07-12T12:42:09,437 copying build/lib.linux-armv7l-3.9/molmod/examples/000_units/a_reaction.py -> build/bdist.linux-armv7l/wheel/molmod/examples/000_units 2021-07-12T12:42:09,440 creating build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:09,442 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/b_dopamine_types.py -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:09,444 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/propane.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:09,447 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/a_propane_types.py -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:09,450 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/mfi_fragment.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:09,453 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/dopamine.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:09,456 creating build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:09,458 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/c_carbon.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:09,460 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/d_size.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:09,463 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/e_shape.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:09,466 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/b_com.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:09,468 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/a_convert.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:09,471 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/ibuprofen.sdf -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:09,474 copying build/lib.linux-armv7l-3.9/molmod/constants.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,477 copying build/lib.linux-armv7l-3.9/molmod/units.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:09,480 running install_egg_info 2021-07-12T12:42:09,487 Copying molmod.egg-info to build/bdist.linux-armv7l/wheel/molmod-1.3.3-py3.9.egg-info 2021-07-12T12:42:09,502 running install_scripts 2021-07-12T12:42:09,563 adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") 2021-07-12T12:42:09,569 creating build/bdist.linux-armv7l/wheel/molmod-1.3.3.dist-info/WHEEL 2021-07-12T12:42:09,572 creating '/tmp/pip-wheel-c1eqgrpn/molmod-1.3.3-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-12T12:42:09,577 adding 'molmod/__init__.py' 2021-07-12T12:42:09,579 adding 'molmod/binning.py' 2021-07-12T12:42:09,582 adding 'molmod/bonds.py' 2021-07-12T12:42:09,584 adding 'molmod/clusters.py' 2021-07-12T12:42:09,586 adding 'molmod/common.c' 2021-07-12T12:42:09,588 adding 'molmod/common.h' 2021-07-12T12:42:09,590 adding 'molmod/constants.py' 2021-07-12T12:42:09,820 adding 'molmod/ext.cpython-39-arm-linux-gnueabihf.so' 2021-07-12T12:42:09,832 adding 'molmod/ext.pyx' 2021-07-12T12:42:09,834 adding 'molmod/ff.c' 2021-07-12T12:42:09,835 adding 'molmod/ff.h' 2021-07-12T12:42:09,837 adding 'molmod/ff.pxd' 2021-07-12T12:42:09,839 adding 'molmod/graphs.c' 2021-07-12T12:42:09,841 adding 'molmod/graphs.h' 2021-07-12T12:42:09,843 adding 'molmod/graphs.pxd' 2021-07-12T12:42:09,853 adding 'molmod/graphs.py' 2021-07-12T12:42:09,858 adding 'molmod/ic.py' 2021-07-12T12:42:09,861 adding 'molmod/isotopes.py' 2021-07-12T12:42:09,864 adding 'molmod/log.py' 2021-07-12T12:42:09,873 adding 'molmod/minimizer.py' 2021-07-12T12:42:09,877 adding 'molmod/molecular_graphs.py' 2021-07-12T12:42:09,879 adding 'molmod/molecules.c' 2021-07-12T12:42:09,881 adding 'molmod/molecules.h' 2021-07-12T12:42:09,882 adding 'molmod/molecules.pxd' 2021-07-12T12:42:09,885 adding 'molmod/molecules.py' 2021-07-12T12:42:09,887 adding 'molmod/pairff.py' 2021-07-12T12:42:09,889 adding 'molmod/periodic.py' 2021-07-12T12:42:09,891 adding 'molmod/quaternions.py' 2021-07-12T12:42:09,894 adding 'molmod/randomize.py' 2021-07-12T12:42:09,896 adding 'molmod/similarity.c' 2021-07-12T12:42:09,898 adding 'molmod/similarity.h' 2021-07-12T12:42:09,900 adding 'molmod/similarity.pxd' 2021-07-12T12:42:09,902 adding 'molmod/similarity.py' 2021-07-12T12:42:09,903 adding 'molmod/symmetry.py' 2021-07-12T12:42:09,906 adding 'molmod/toyff.py' 2021-07-12T12:42:09,909 adding 'molmod/transformations.py' 2021-07-12T12:42:09,911 adding 'molmod/unit_cells.c' 2021-07-12T12:42:09,913 adding 'molmod/unit_cells.h' 2021-07-12T12:42:09,914 adding 'molmod/unit_cells.pxd' 2021-07-12T12:42:09,917 adding 'molmod/unit_cells.py' 2021-07-12T12:42:09,919 adding 'molmod/units.py' 2021-07-12T12:42:09,922 adding 'molmod/utils.py' 2021-07-12T12:42:09,924 adding 'molmod/vectors.py' 2021-07-12T12:42:09,925 adding 'molmod/version.py' 2021-07-12T12:42:09,927 adding 'molmod/zmatrix.py' 2021-07-12T12:42:09,930 adding 'molmod/data/bonds.csv' 2021-07-12T12:42:09,933 adding 'molmod/data/bonds.ods' 2021-07-12T12:42:10,019 adding 'molmod/data/mass.mas03' 2021-07-12T12:42:10,106 adding 'molmod/data/nubtab03.asc' 2021-07-12T12:42:10,112 adding 'molmod/data/periodic.csv' 2021-07-12T12:42:10,116 adding 'molmod/data/periodic.ods' 2021-07-12T12:42:10,131 adding 'molmod/data/toyff_angles.txt' 2021-07-12T12:42:10,139 adding 'molmod/data/test/1LJL_Cys10.cml' 2021-07-12T12:42:10,274 adding 'molmod/data/test/1TOH.b3lyp.fchk' 2021-07-12T12:42:10,280 adding 'molmod/data/test/1TOH.b3lyp.trim.fchk' 2021-07-12T12:42:10,282 adding 'molmod/data/test/5ringOH.xyz' 2021-07-12T12:42:10,284 adding 'molmod/data/test/CID_22898828.sdf' 2021-07-12T12:42:10,533 adding 'molmod/data/test/PCGamess_PUNCH' 2021-07-12T12:42:10,542 adding 'molmod/data/test/SID_31646545.sdf' 2021-07-12T12:42:10,543 adding 'molmod/data/test/SID_31646548.sdf' 2021-07-12T12:42:10,545 adding 'molmod/data/test/SID_40363570.sdf' 2021-07-12T12:42:10,547 adding 'molmod/data/test/SID_40363571.sdf' 2021-07-12T12:42:10,549 adding 'molmod/data/test/SID_41893278.sdf' 2021-07-12T12:42:10,550 adding 'molmod/data/test/SID_41893280.sdf' 2021-07-12T12:42:10,552 adding 'molmod/data/test/SID_54258192.sdf' 2021-07-12T12:42:10,554 adding 'molmod/data/test/SID_55127927.sdf' 2021-07-12T12:42:10,556 adding 'molmod/data/test/SID_55488598.sdf' 2021-07-12T12:42:10,558 adding 'molmod/data/test/SID_56274343.sdf' 2021-07-12T12:42:10,559 adding 'molmod/data/test/TRAJECTORY_H2_CPMD' 2021-07-12T12:42:10,563 adding 'molmod/data/test/alanine.cube' 2021-07-12T12:42:10,565 adding 'molmod/data/test/argon.xyz' 2021-07-12T12:42:10,643 adding 'molmod/data/test/bartek.atrj' 2021-07-12T12:42:10,648 adding 'molmod/data/test/benzene.xyz' 2021-07-12T12:42:10,649 adding 'molmod/data/test/butane.xyz' 2021-07-12T12:42:10,651 adding 'molmod/data/test/caplayer.cml' 2021-07-12T12:42:10,720 adding 'molmod/data/test/crystal_api.out' 2021-07-12T12:42:10,725 adding 'molmod/data/test/cyclopentane.xyz' 2021-07-12T12:42:10,726 adding 'molmod/data/test/dinitrogen.xyz' 2021-07-12T12:42:10,728 adding 'molmod/data/test/dlpoly_HISTORY' 2021-07-12T12:42:10,730 adding 'molmod/data/test/dlpoly_HISTORY_an2' 2021-07-12T12:42:10,735 adding 'molmod/data/test/dlpoly_OUTPUT' 2021-07-12T12:42:10,737 adding 'molmod/data/test/dopamine.xyz' 2021-07-12T12:42:10,738 adding 'molmod/data/test/ethane.xyz' 2021-07-12T12:42:10,740 adding 'molmod/data/test/ethene.xyz' 2021-07-12T12:42:10,741 adding 'molmod/data/test/ethene_ethyl_trans.xyz' 2021-07-12T12:42:10,743 adding 'molmod/data/test/example.sdf' 2021-07-12T12:42:10,744 adding 'molmod/data/test/formol.xyz' 2021-07-12T12:42:10,746 adding 'molmod/data/test/funny.xyz' 2021-07-12T12:42:10,748 adding 'molmod/data/test/h3zrosihohosioh3.xyz' 2021-07-12T12:42:10,778 adding 'molmod/data/test/il2.pdb' 2021-07-12T12:42:10,783 adding 'molmod/data/test/lammps_dump.txt' 2021-07-12T12:42:10,785 adding 'molmod/data/test/lau.xyz' 2021-07-12T12:42:10,786 adding 'molmod/data/test/octane.xyz' 2021-07-12T12:42:10,788 adding 'molmod/data/test/oh3siozroh3.xyz' 2021-07-12T12:42:10,790 adding 'molmod/data/test/opt_5ring10T.xyz' 2021-07-12T12:42:10,791 adding 'molmod/data/test/opt_5ring12T.xyz' 2021-07-12T12:42:10,793 adding 'molmod/data/test/opt_6_6ring.xyz' 2021-07-12T12:42:10,795 adding 'molmod/data/test/opt_6ring.xyz' 2021-07-12T12:42:10,797 adding 'molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz' 2021-07-12T12:42:10,799 adding 'molmod/data/test/pentapeptide.psf' 2021-07-12T12:42:10,801 adding 'molmod/data/test/precursor.xyz' 2021-07-12T12:42:10,803 adding 'molmod/data/test/probes.xyz' 2021-07-12T12:42:10,804 adding 'molmod/data/test/tea.xyz' 2021-07-12T12:42:10,806 adding 'molmod/data/test/tetra.xyz' 2021-07-12T12:42:10,828 adding 'molmod/data/test/thf.psf' 2021-07-12T12:42:10,836 adding 'molmod/data/test/thf.xyz' 2021-07-12T12:42:10,838 adding 'molmod/data/test/thf_64.cell' 2021-07-12T12:42:10,839 adding 'molmod/data/test/thf_single.xyz' 2021-07-12T12:42:10,841 adding 'molmod/data/test/tpa.xyz' 2021-07-12T12:42:10,842 adding 'molmod/data/test/water.xyz' 2021-07-12T12:42:10,844 adding 'molmod/data/test/water2.gro' 2021-07-12T12:42:10,845 adding 'molmod/data/test/water_md.inp' 2021-07-12T12:42:10,846 adding 'molmod/data/test/zr4o8-3.xyz' 2021-07-12T12:42:10,849 adding 'molmod/examples/000_units/a_reaction.py' 2021-07-12T12:42:10,851 adding 'molmod/examples/000_units/b_chbond.py' 2021-07-12T12:42:10,852 adding 'molmod/examples/000_units/c_h2rot.py' 2021-07-12T12:42:10,854 adding 'molmod/examples/001_molecules/a_convert.py' 2021-07-12T12:42:10,855 adding 'molmod/examples/001_molecules/b_com.py' 2021-07-12T12:42:10,857 adding 'molmod/examples/001_molecules/c_carbon.py' 2021-07-12T12:42:10,858 adding 'molmod/examples/001_molecules/d_size.py' 2021-07-12T12:42:10,860 adding 'molmod/examples/001_molecules/e_shape.py' 2021-07-12T12:42:10,861 adding 'molmod/examples/001_molecules/ibuprofen.sdf' 2021-07-12T12:42:10,864 adding 'molmod/examples/002_graphs/a_graphs.py' 2021-07-12T12:42:10,865 adding 'molmod/examples/002_graphs/b_neighbors.py' 2021-07-12T12:42:10,866 adding 'molmod/examples/002_graphs/c_distances.py' 2021-07-12T12:42:10,868 adding 'molmod/examples/002_graphs/caffeine.xyz' 2021-07-12T12:42:10,869 adding 'molmod/examples/002_graphs/d_symmetries.py' 2021-07-12T12:42:10,870 adding 'molmod/examples/002_graphs/ethanol.xyz' 2021-07-12T12:42:10,872 adding 'molmod/examples/003_internal_coordinates/a_bond_length.py' 2021-07-12T12:42:10,874 adding 'molmod/examples/003_internal_coordinates/b_bending_angles.py' 2021-07-12T12:42:10,876 adding 'molmod/examples/003_internal_coordinates/c_ff_hessian.py' 2021-07-12T12:42:10,878 adding 'molmod/examples/003_internal_coordinates/d_dft_hessian.py' 2021-07-12T12:42:10,889 adding 'molmod/examples/003_internal_coordinates/dopamine.fchk' 2021-07-12T12:42:10,890 adding 'molmod/examples/003_internal_coordinates/dopamine.xyz' 2021-07-12T12:42:10,892 adding 'molmod/examples/003_internal_coordinates/propane.xyz' 2021-07-12T12:42:10,894 adding 'molmod/examples/004_patterns/a_propane_types.py' 2021-07-12T12:42:10,895 adding 'molmod/examples/004_patterns/b_dopamine_types.py' 2021-07-12T12:42:10,896 adding 'molmod/examples/004_patterns/dopamine.xyz' 2021-07-12T12:42:10,898 adding 'molmod/examples/004_patterns/mfi_fragment.xyz' 2021-07-12T12:42:10,899 adding 'molmod/examples/004_patterns/propane.xyz' 2021-07-12T12:42:10,902 adding 'molmod/io/__init__.py' 2021-07-12T12:42:10,903 adding 'molmod/io/atrj.py' 2021-07-12T12:42:10,905 adding 'molmod/io/chk.py' 2021-07-12T12:42:10,907 adding 'molmod/io/cml.py' 2021-07-12T12:42:10,908 adding 'molmod/io/common.py' 2021-07-12T12:42:10,911 adding 'molmod/io/cp2k.py' 2021-07-12T12:42:10,912 adding 'molmod/io/cpmd.py' 2021-07-12T12:42:10,914 adding 'molmod/io/crystal.py' 2021-07-12T12:42:10,916 adding 'molmod/io/cube.py' 2021-07-12T12:42:10,918 adding 'molmod/io/dlpoly.py' 2021-07-12T12:42:10,920 adding 'molmod/io/fchk.py' 2021-07-12T12:42:10,922 adding 'molmod/io/gamess.py' 2021-07-12T12:42:10,923 adding 'molmod/io/gromacs.py' 2021-07-12T12:42:10,925 adding 'molmod/io/lammps.py' 2021-07-12T12:42:10,927 adding 'molmod/io/number_state.py' 2021-07-12T12:42:10,929 adding 'molmod/io/pdb.py' 2021-07-12T12:42:10,931 adding 'molmod/io/psf.py' 2021-07-12T12:42:10,933 adding 'molmod/io/sdf.py' 2021-07-12T12:42:10,934 adding 'molmod/io/xyz.py' 2021-07-12T12:42:10,937 adding 'molmod/io/test/__init__.py' 2021-07-12T12:42:10,938 adding 'molmod/io/test/test_atrj.py' 2021-07-12T12:42:10,940 adding 'molmod/io/test/test_cml.py' 2021-07-12T12:42:10,941 adding 'molmod/io/test/test_cp2k.py' 2021-07-12T12:42:10,943 adding 'molmod/io/test/test_cpmd.py' 2021-07-12T12:42:10,944 adding 'molmod/io/test/test_crystal.py' 2021-07-12T12:42:10,946 adding 'molmod/io/test/test_cube.py' 2021-07-12T12:42:10,947 adding 'molmod/io/test/test_dlpoly.py' 2021-07-12T12:42:10,949 adding 'molmod/io/test/test_fchk.py' 2021-07-12T12:42:10,950 adding 'molmod/io/test/test_gamess.py' 2021-07-12T12:42:10,951 adding 'molmod/io/test/test_gromacs.py' 2021-07-12T12:42:10,953 adding 'molmod/io/test/test_lammps.py' 2021-07-12T12:42:10,954 adding 'molmod/io/test/test_number_state.py' 2021-07-12T12:42:10,956 adding 'molmod/io/test/test_pdb.py' 2021-07-12T12:42:10,957 adding 'molmod/io/test/test_psf.py' 2021-07-12T12:42:10,959 adding 'molmod/io/test/test_sdf.py' 2021-07-12T12:42:10,960 adding 'molmod/io/test/test_xyz.py' 2021-07-12T12:42:10,962 adding 'molmod/test/__init__.py' 2021-07-12T12:42:10,964 adding 'molmod/test/common.py' 2021-07-12T12:42:10,966 adding 'molmod/test/test_binning.py' 2021-07-12T12:42:10,967 adding 'molmod/test/test_clusters.py' 2021-07-12T12:42:10,969 adding 'molmod/test/test_data.py' 2021-07-12T12:42:10,970 adding 'molmod/test/test_examples.py' 2021-07-12T12:42:10,975 adding 'molmod/test/test_graphs.py' 2021-07-12T12:42:10,977 adding 'molmod/test/test_ic.py' 2021-07-12T12:42:10,978 adding 'molmod/test/test_log.py' 2021-07-12T12:42:10,981 adding 'molmod/test/test_minimizer.py' 2021-07-12T12:42:10,984 adding 'molmod/test/test_molecular_graphs.py' 2021-07-12T12:42:10,987 adding 'molmod/test/test_molecules.py' 2021-07-12T12:42:10,990 adding 'molmod/test/test_pairff.py' 2021-07-12T12:42:10,992 adding 'molmod/test/test_quaternions.py' 2021-07-12T12:42:10,993 adding 'molmod/test/test_randomize.py' 2021-07-12T12:42:10,995 adding 'molmod/test/test_similarity.py' 2021-07-12T12:42:10,997 adding 'molmod/test/test_symmetry.py' 2021-07-12T12:42:11,000 adding 'molmod/test/test_toyff.py' 2021-07-12T12:42:11,002 adding 'molmod/test/test_transformations.py' 2021-07-12T12:42:11,005 adding 'molmod/test/test_unit_cells.py' 2021-07-12T12:42:11,007 adding 'molmod/test/test_units.py' 2021-07-12T12:42:11,009 adding 'molmod/test/test_utils.py' 2021-07-12T12:42:11,010 adding 'molmod/test/test_vectors.py' 2021-07-12T12:42:11,012 adding 'molmod/test/test_zmatrix.py' 2021-07-12T12:42:11,020 adding 'molmod-1.3.3.dist-info/LICENSE.txt' 2021-07-12T12:42:11,021 adding 'molmod-1.3.3.dist-info/METADATA' 2021-07-12T12:42:11,022 adding 'molmod-1.3.3.dist-info/WHEEL' 2021-07-12T12:42:11,023 adding 'molmod-1.3.3.dist-info/top_level.txt' 2021-07-12T12:42:11,026 adding 'molmod-1.3.3.dist-info/RECORD' 2021-07-12T12:42:11,061 removing build/bdist.linux-armv7l/wheel 2021-07-12T12:42:11,556 Building wheel for molmod (setup.py): finished with status 'done' 2021-07-12T12:42:11,586 Created wheel for molmod: filename=molmod-1.3.3-cp39-cp39-linux_armv7l.whl size=1953942 sha256=c955105191874f6641662739e86d8ce23f438ab2f28a36a36cb8943a4ce21ea0 2021-07-12T12:42:11,586 Stored in directory: /tmp/pip-ephem-wheel-cache-gk0i7eyb/wheels/cb/99/d0/876ceb403f1b42381571be1fca0beca4c28780a364989d7a1d 2021-07-12T12:42:11,605 Successfully built molmod 2021-07-12T12:42:11,682 Removed build tracker: '/tmp/pip-req-tracker-cajdw6bu'