2021-07-12T12:41:30,429 Created temporary directory: /tmp/pip-ephem-wheel-cache-jbg47v5j 2021-07-12T12:41:30,432 Created temporary directory: /tmp/pip-req-tracker-l4jtce6j 2021-07-12T12:41:30,432 Initialized build tracking at /tmp/pip-req-tracker-l4jtce6j 2021-07-12T12:41:30,433 Created build tracker: /tmp/pip-req-tracker-l4jtce6j 2021-07-12T12:41:30,433 Entered build tracker: /tmp/pip-req-tracker-l4jtce6j 2021-07-12T12:41:30,433 Created temporary directory: /tmp/pip-wheel-gfqchnil 2021-07-12T12:41:30,462 1 location(s) to search for versions of molmod: 2021-07-12T12:41:30,462 * https://pypi.org/simple/molmod/ 2021-07-12T12:41:30,463 Fetching project page and analyzing links: https://pypi.org/simple/molmod/ 2021-07-12T12:41:30,463 Getting page https://pypi.org/simple/molmod/ 2021-07-12T12:41:30,465 Found index url https://pypi.org/simple 2021-07-12T12:41:30,558 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 2021-07-12T12:41:30,558 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 2021-07-12T12:41:30,558 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 2021-07-12T12:41:30,559 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 2021-07-12T12:41:30,559 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 2021-07-12T12:41:30,559 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 2021-07-12T12:41:30,560 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 2021-07-12T12:41:30,560 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 2021-07-12T12:41:30,560 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 2021-07-12T12:41:30,560 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 2021-07-12T12:41:30,561 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 2021-07-12T12:41:30,561 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 2021-07-12T12:41:30,561 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 2021-07-12T12:41:30,562 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 2021-07-12T12:41:30,562 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 2021-07-12T12:41:30,562 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 2021-07-12T12:41:30,562 Skipping link: not a file: https://pypi.org/simple/molmod/ 2021-07-12T12:41:30,582 Given no hashes to check 1 links for project 'molmod': discarding no candidates 2021-07-12T12:41:30,601 Collecting molmod==1.3.2 2021-07-12T12:41:30,603 Created temporary directory: /tmp/pip-unpack-qd55d6eq 2021-07-12T12:41:31,419 Downloading molmod-1.3.2.tar.gz (1.7 MB) 2021-07-12T12:41:32,355 Added molmod==1.3.2 from https://files.pythonhosted.org/packages/79/fd/9f4282bf37b3ee38242dc4c6883b0923d450331f491ab5942702b791e84a/molmod-1.3.2.tar.gz#sha256=0af0b797cf628458e1f5c0334cf7f7f1c2ee6a3edbba87ca0fbde39e9b444ec7 to build tracker '/tmp/pip-req-tracker-l4jtce6j' 2021-07-12T12:41:32,356 Running setup.py (path:/tmp/pip-wheel-gfqchnil/molmod_86c45eb1e09d4663a7a9974f28dd4737/setup.py) egg_info for package molmod 2021-07-12T12:41:32,357 Created temporary directory: /tmp/pip-pip-egg-info-cb06csxo 2021-07-12T12:41:32,358 Running command python setup.py egg_info 2021-07-12T12:41:34,353 fatal: not a git repository (or any of the parent directories): .git 2021-07-12T12:41:34,569 running egg_info 2021-07-12T12:41:34,571 creating /tmp/pip-pip-egg-info-cb06csxo/molmod.egg-info 2021-07-12T12:41:34,572 writing /tmp/pip-pip-egg-info-cb06csxo/molmod.egg-info/PKG-INFO 2021-07-12T12:41:34,575 writing dependency_links to /tmp/pip-pip-egg-info-cb06csxo/molmod.egg-info/dependency_links.txt 2021-07-12T12:41:34,577 writing requirements to /tmp/pip-pip-egg-info-cb06csxo/molmod.egg-info/requires.txt 2021-07-12T12:41:34,578 writing top-level names to /tmp/pip-pip-egg-info-cb06csxo/molmod.egg-info/top_level.txt 2021-07-12T12:41:34,579 writing manifest file '/tmp/pip-pip-egg-info-cb06csxo/molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:34,770 reading manifest file '/tmp/pip-pip-egg-info-cb06csxo/molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:34,773 reading manifest template 'MANIFEST.in' 2021-07-12T12:41:35,128 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2021-07-12T12:41:35,185 adding license file 'LICENSE.txt' 2021-07-12T12:41:35,195 writing manifest file '/tmp/pip-pip-egg-info-cb06csxo/molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:35,321 Source in /tmp/pip-wheel-gfqchnil/molmod_86c45eb1e09d4663a7a9974f28dd4737 has version 1.3.2, which satisfies requirement molmod==1.3.2 from https://files.pythonhosted.org/packages/79/fd/9f4282bf37b3ee38242dc4c6883b0923d450331f491ab5942702b791e84a/molmod-1.3.2.tar.gz#sha256=0af0b797cf628458e1f5c0334cf7f7f1c2ee6a3edbba87ca0fbde39e9b444ec7 2021-07-12T12:41:35,321 Removed molmod==1.3.2 from https://files.pythonhosted.org/packages/79/fd/9f4282bf37b3ee38242dc4c6883b0923d450331f491ab5942702b791e84a/molmod-1.3.2.tar.gz#sha256=0af0b797cf628458e1f5c0334cf7f7f1c2ee6a3edbba87ca0fbde39e9b444ec7 from build tracker '/tmp/pip-req-tracker-l4jtce6j' 2021-07-12T12:41:35,325 Created temporary directory: /tmp/pip-unpack-giwxivbs 2021-07-12T12:41:35,326 Building wheels for collected packages: molmod 2021-07-12T12:41:35,330 Created temporary directory: /tmp/pip-wheel-aiu3ubwh 2021-07-12T12:41:35,331 Building wheel for molmod (setup.py): started 2021-07-12T12:41:35,331 Destination directory: /tmp/pip-wheel-aiu3ubwh 2021-07-12T12:41:35,331 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-gfqchnil/molmod_86c45eb1e09d4663a7a9974f28dd4737/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-gfqchnil/molmod_86c45eb1e09d4663a7a9974f28dd4737/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-aiu3ubwh 2021-07-12T12:41:36,737 fatal: not a git repository (or any of the parent directories): .git 2021-07-12T12:41:36,957 running bdist_wheel 2021-07-12T12:41:36,962 running build 2021-07-12T12:41:36,962 running build_py 2021-07-12T12:41:37,098 creating build 2021-07-12T12:41:37,098 creating build/lib.linux-armv7l-3.9 2021-07-12T12:41:37,099 creating build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,100 copying molmod/log.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,103 copying molmod/vectors.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,105 copying molmod/graphs.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,108 copying molmod/toyff.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,111 copying molmod/ic.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,114 copying molmod/version.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,115 copying molmod/similarity.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,118 copying molmod/clusters.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,120 copying molmod/utils.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,123 copying molmod/__init__.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,124 copying molmod/pairff.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,127 copying molmod/minimizer.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,131 copying molmod/molecular_graphs.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,134 copying molmod/bonds.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,137 copying molmod/symmetry.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,138 copying molmod/periodic.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,141 copying molmod/isotopes.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,143 copying molmod/unit_cells.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,146 copying molmod/units.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,148 copying molmod/zmatrix.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,151 copying molmod/molecules.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,154 copying molmod/binning.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,157 copying molmod/quaternions.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,159 copying molmod/randomize.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,161 copying molmod/constants.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,163 copying molmod/transformations.py -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,168 creating build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,169 copying molmod/test/test_transformations.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,172 copying molmod/test/test_graphs.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,175 copying molmod/test/test_examples.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,177 copying molmod/test/test_minimizer.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,180 copying molmod/test/test_randomize.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,182 copying molmod/test/test_clusters.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,184 copying molmod/test/test_data.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,186 copying molmod/test/test_quaternions.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,188 copying molmod/test/test_similarity.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,190 copying molmod/test/__init__.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,192 copying molmod/test/common.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,194 copying molmod/test/test_unit_cells.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,197 copying molmod/test/test_ic.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,199 copying molmod/test/test_binning.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,202 copying molmod/test/test_molecular_graphs.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,205 copying molmod/test/test_symmetry.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,206 copying molmod/test/test_units.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,208 copying molmod/test/test_log.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,210 copying molmod/test/test_pairff.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,213 copying molmod/test/test_zmatrix.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,215 copying molmod/test/test_toyff.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,217 copying molmod/test/test_molecules.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,219 copying molmod/test/test_vectors.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,221 copying molmod/test/test_utils.py -> build/lib.linux-armv7l-3.9/molmod/test 2021-07-12T12:41:37,225 creating build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,226 copying molmod/io/cp2k.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,228 copying molmod/io/gromacs.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,231 copying molmod/io/chk.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,233 copying molmod/io/pdb.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,235 copying molmod/io/dlpoly.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,238 copying molmod/io/fchk.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,240 copying molmod/io/xyz.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,243 copying molmod/io/__init__.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,245 copying molmod/io/common.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,247 copying molmod/io/lammps.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,249 copying molmod/io/cml.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,251 copying molmod/io/cpmd.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,253 copying molmod/io/crystal.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,255 copying molmod/io/atrj.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,258 copying molmod/io/gamess.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,261 copying molmod/io/number_state.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,263 copying molmod/io/psf.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,266 copying molmod/io/cube.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,268 copying molmod/io/sdf.py -> build/lib.linux-armv7l-3.9/molmod/io 2021-07-12T12:41:37,272 creating build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,273 copying molmod/io/test/test_crystal.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,275 copying molmod/io/test/test_pdb.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,277 copying molmod/io/test/test_xyz.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,280 copying molmod/io/test/test_dlpoly.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,281 copying molmod/io/test/test_sdf.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,283 copying molmod/io/test/__init__.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,285 copying molmod/io/test/test_cube.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,288 copying molmod/io/test/test_number_state.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,290 copying molmod/io/test/test_cp2k.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,293 copying molmod/io/test/test_lammps.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,295 copying molmod/io/test/test_gromacs.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,297 copying molmod/io/test/test_gamess.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,299 copying molmod/io/test/test_cpmd.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,301 copying molmod/io/test/test_psf.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,303 copying molmod/io/test/test_fchk.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,305 copying molmod/io/test/test_atrj.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,307 copying molmod/io/test/test_cml.py -> build/lib.linux-armv7l-3.9/molmod/io/test 2021-07-12T12:41:37,308 running egg_info 2021-07-12T12:41:37,325 writing molmod.egg-info/PKG-INFO 2021-07-12T12:41:37,327 writing dependency_links to molmod.egg-info/dependency_links.txt 2021-07-12T12:41:37,329 writing requirements to molmod.egg-info/requires.txt 2021-07-12T12:41:37,331 writing top-level names to molmod.egg-info/top_level.txt 2021-07-12T12:41:37,395 reading manifest file 'molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:37,404 reading manifest template 'MANIFEST.in' 2021-07-12T12:41:37,782 warning: no previously-included files matching 'ext.c' found under directory 'molmod' 2021-07-12T12:41:37,842 adding license file 'LICENSE.txt' 2021-07-12T12:41:37,858 writing manifest file 'molmod.egg-info/SOURCES.txt' 2021-07-12T12:41:37,875 copying molmod/common.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,877 copying molmod/common.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,879 copying molmod/ext.pyx -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,881 copying molmod/ff.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,883 copying molmod/ff.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,885 copying molmod/ff.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,887 copying molmod/graphs.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,890 copying molmod/graphs.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,892 copying molmod/graphs.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,894 copying molmod/molecules.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,896 copying molmod/molecules.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,899 copying molmod/molecules.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,901 copying molmod/similarity.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,903 copying molmod/similarity.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,906 copying molmod/similarity.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,908 copying molmod/unit_cells.c -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,911 copying molmod/unit_cells.h -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,913 copying molmod/unit_cells.pxd -> build/lib.linux-armv7l-3.9/molmod 2021-07-12T12:41:37,915 creating build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:37,916 copying molmod/data/bonds.csv -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:37,919 copying molmod/data/bonds.ods -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:37,922 copying molmod/data/mass.mas03 -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:37,935 copying molmod/data/nubtab03.asc -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:37,950 copying molmod/data/periodic.csv -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:37,953 copying molmod/data/periodic.ods -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:37,957 copying molmod/data/toyff_angles.txt -> build/lib.linux-armv7l-3.9/molmod/data 2021-07-12T12:41:37,960 creating build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:37,961 copying molmod/data/test/1LJL_Cys10.cml -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:37,965 copying molmod/data/test/1TOH.b3lyp.fchk -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:37,981 copying molmod/data/test/1TOH.b3lyp.trim.fchk -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:37,984 copying molmod/data/test/5ringOH.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:37,986 copying molmod/data/test/CID_22898828.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:37,988 copying molmod/data/test/PCGamess_PUNCH -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,015 copying molmod/data/test/SID_31646545.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,018 copying molmod/data/test/SID_31646548.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,020 copying molmod/data/test/SID_40363570.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,023 copying molmod/data/test/SID_40363571.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,025 copying molmod/data/test/SID_41893278.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,028 copying molmod/data/test/SID_41893280.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,031 copying molmod/data/test/SID_54258192.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,033 copying molmod/data/test/SID_55127927.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,036 copying molmod/data/test/SID_55488598.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,038 copying molmod/data/test/SID_56274343.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,041 copying molmod/data/test/TRAJECTORY_H2_CPMD -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,044 copying molmod/data/test/alanine.cube -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,048 copying molmod/data/test/argon.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,050 copying molmod/data/test/bartek.atrj -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,063 copying molmod/data/test/benzene.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,065 copying molmod/data/test/butane.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,068 copying molmod/data/test/caplayer.cml -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,071 copying molmod/data/test/crystal_api.out -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,084 copying molmod/data/test/cyclopentane.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,086 copying molmod/data/test/dinitrogen.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,088 copying molmod/data/test/dlpoly_HISTORY -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,091 copying molmod/data/test/dlpoly_HISTORY_an2 -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,093 copying molmod/data/test/dlpoly_OUTPUT -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,096 copying molmod/data/test/dopamine.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,098 copying molmod/data/test/ethane.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,101 copying molmod/data/test/ethene.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,103 copying molmod/data/test/ethene_ethyl_trans.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,105 copying molmod/data/test/example.sdf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,107 copying molmod/data/test/formol.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,110 copying molmod/data/test/funny.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,112 copying molmod/data/test/h3zrosihohosioh3.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,114 copying molmod/data/test/il2.pdb -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,121 copying molmod/data/test/lammps_dump.txt -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,124 copying molmod/data/test/lau.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,126 copying molmod/data/test/octane.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,128 copying molmod/data/test/oh3siozroh3.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,131 copying molmod/data/test/opt_5ring10T.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,133 copying molmod/data/test/opt_5ring12T.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,136 copying molmod/data/test/opt_6_6ring.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,138 copying molmod/data/test/opt_6ring.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,141 copying molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,143 copying molmod/data/test/pentapeptide.psf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,146 copying molmod/data/test/precursor.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,149 copying molmod/data/test/probes.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,152 copying molmod/data/test/tea.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,154 copying molmod/data/test/tetra.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,156 copying molmod/data/test/thf.psf -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,164 copying molmod/data/test/thf.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,169 copying molmod/data/test/thf_64.cell -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,172 copying molmod/data/test/thf_single.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,174 copying molmod/data/test/tpa.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,176 copying molmod/data/test/water.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,180 copying molmod/data/test/water2.gro -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,182 copying molmod/data/test/water_md.inp -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,184 copying molmod/data/test/zr4o8-3.xyz -> build/lib.linux-armv7l-3.9/molmod/data/test 2021-07-12T12:41:38,187 creating build/lib.linux-armv7l-3.9/molmod/examples 2021-07-12T12:41:38,187 creating build/lib.linux-armv7l-3.9/molmod/examples/000_units 2021-07-12T12:41:38,188 copying molmod/examples/000_units/a_reaction.py -> build/lib.linux-armv7l-3.9/molmod/examples/000_units 2021-07-12T12:41:38,191 copying molmod/examples/000_units/b_chbond.py -> build/lib.linux-armv7l-3.9/molmod/examples/000_units 2021-07-12T12:41:38,193 copying molmod/examples/000_units/c_h2rot.py -> build/lib.linux-armv7l-3.9/molmod/examples/000_units 2021-07-12T12:41:38,196 creating build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:38,197 copying molmod/examples/001_molecules/a_convert.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:38,199 copying molmod/examples/001_molecules/b_com.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:38,202 copying molmod/examples/001_molecules/c_carbon.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:38,204 copying molmod/examples/001_molecules/d_size.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:38,206 copying molmod/examples/001_molecules/e_shape.py -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:38,209 copying molmod/examples/001_molecules/ibuprofen.sdf -> build/lib.linux-armv7l-3.9/molmod/examples/001_molecules 2021-07-12T12:41:38,212 creating build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:38,213 copying molmod/examples/002_graphs/a_graphs.py -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:38,215 copying molmod/examples/002_graphs/b_neighbors.py -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:38,218 copying molmod/examples/002_graphs/c_distances.py -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:38,220 copying molmod/examples/002_graphs/caffeine.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:38,222 copying molmod/examples/002_graphs/d_symmetries.py -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:38,225 copying molmod/examples/002_graphs/ethanol.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/002_graphs 2021-07-12T12:41:38,227 creating build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:38,228 copying molmod/examples/003_internal_coordinates/a_bond_length.py -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:38,230 copying molmod/examples/003_internal_coordinates/b_bending_angles.py -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:38,233 copying molmod/examples/003_internal_coordinates/c_ff_hessian.py -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:38,236 copying molmod/examples/003_internal_coordinates/d_dft_hessian.py -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:38,238 copying molmod/examples/003_internal_coordinates/dopamine.fchk -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:38,243 copying molmod/examples/003_internal_coordinates/dopamine.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:38,245 copying molmod/examples/003_internal_coordinates/propane.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates 2021-07-12T12:41:38,247 creating build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:38,248 copying molmod/examples/004_patterns/a_propane_types.py -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:38,251 copying molmod/examples/004_patterns/b_dopamine_types.py -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:38,253 copying molmod/examples/004_patterns/dopamine.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:38,255 copying molmod/examples/004_patterns/mfi_fragment.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:38,258 copying molmod/examples/004_patterns/propane.xyz -> build/lib.linux-armv7l-3.9/molmod/examples/004_patterns 2021-07-12T12:41:38,269 running build_ext 2021-07-12T12:41:38,275 cythoning molmod/ext.pyx to molmod/ext.c 2021-07-12T12:41:38,884 /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-gfqchnil/molmod_86c45eb1e09d4663a7a9974f28dd4737/molmod/ext.pyx 2021-07-12T12:41:38,885 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-12T12:41:46,249 building 'molmod.ext' extension 2021-07-12T12:41:46,250 creating build/temp.linux-armv7l-3.9 2021-07-12T12:41:46,250 creating build/temp.linux-armv7l-3.9/molmod 2021-07-12T12:41:46,251 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 2021-07-12T12:41:46,493 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 2021-07-12T12:41:46,897 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-12T12:41:46,898 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-12T12:41:46,898 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-12T12:41:46,898 from molmod/ext.c:612: 2021-07-12T12:41:46,898 /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] 2021-07-12T12:41:46,898 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-12T12:41:46,899 | ^~~~~~~ 2021-07-12T12:41:46,978 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_ff_dm_quad’: 2021-07-12T12:41:46,980 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] 2021-07-12T12:41:46,980 2923 | __pyx_t_3 = (((__pyx_v_dm0.shape[0]) != __pyx_v_natom) != 0); 2021-07-12T12:41:46,980 | ^~ 2021-07-12T12:41:46,981 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] 2021-07-12T12:41:46,981 2929 | __pyx_t_3 = (((__pyx_v_dm0.shape[1]) != __pyx_v_natom) != 0); 2021-07-12T12:41:46,982 | ^~ 2021-07-12T12:41:46,983 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] 2021-07-12T12:41:46,983 2963 | __pyx_t_3 = (((__pyx_v_dmk.shape[0]) != __pyx_v_natom) != 0); 2021-07-12T12:41:46,983 | ^~ 2021-07-12T12:41:46,984 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] 2021-07-12T12:41:46,984 2969 | __pyx_t_3 = (((__pyx_v_dmk.shape[1]) != __pyx_v_natom) != 0); 2021-07-12T12:41:46,985 | ^~ 2021-07-12T12:41:47,021 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_2ff_dm_reci’: 2021-07-12T12:41:47,023 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] 2021-07-12T12:41:47,023 3679 | __pyx_t_1 = (((__pyx_v_radii.shape[0]) != __pyx_v_natom) != 0); 2021-07-12T12:41:47,023 | ^~ 2021-07-12T12:41:47,025 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] 2021-07-12T12:41:47,025 3711 | __pyx_t_3 = (((__pyx_v_dm0.shape[0]) != __pyx_v_natom) != 0); 2021-07-12T12:41:47,025 | ^~ 2021-07-12T12:41:47,027 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] 2021-07-12T12:41:47,027 3717 | __pyx_t_3 = (((__pyx_v_dm0.shape[1]) != __pyx_v_natom) != 0); 2021-07-12T12:41:47,027 | ^~ 2021-07-12T12:41:47,072 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_4ff_bond_quad’: 2021-07-12T12:41:47,074 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] 2021-07-12T12:41:47,075 4583 | __pyx_t_1 = (((__pyx_v_lengths.shape[0]) != __pyx_v_npair) != 0); 2021-07-12T12:41:47,075 | ^~ 2021-07-12T12:41:47,122 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_6ff_bond_hyper’: 2021-07-12T12:41:47,124 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] 2021-07-12T12:41:47,125 5327 | __pyx_t_1 = (((__pyx_v_lengths.shape[0]) != __pyx_v_npair) != 0); 2021-07-12T12:41:47,125 | ^~ 2021-07-12T12:41:47,173 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_8graphs_floyd_warshall’: 2021-07-12T12:41:47,176 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] 2021-07-12T12:41:47,176 5858 | __pyx_t_1 = (((__pyx_v_dm.shape[1]) != __pyx_v_nvertex) != 0); 2021-07-12T12:41:47,176 | ^~ 2021-07-12T12:41:47,235 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_12similarity_table_labels’: 2021-07-12T12:41:47,238 molmod/ext.c:6700:39: warning: passing argument 2 of ‘similarity_table_labels’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-12T12:41:47,239 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)))); 2021-07-12T12:41:47,239 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T12:41:47,239 In file included from molmod/ext.c:623: 2021-07-12T12:41:47,239 molmod/similarity.h:30:46: note: expected ‘long int *’ but argument is of type ‘const long int *’ 2021-07-12T12:41:47,239 30 | void similarity_table_labels(size_t n, long *labels, long* labels_table); 2021-07-12T12:41:47,239 | ~~~~~~^~~~~~ 2021-07-12T12:41:47,241 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_14similarity_table_distances’: 2021-07-12T12:41:47,244 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] 2021-07-12T12:41:47,244 6831 | __pyx_t_1 = (((__pyx_v_distance_matrix.shape[1]) != __pyx_v_n) != 0); 2021-07-12T12:41:47,244 | ^~ 2021-07-12T12:41:47,259 molmod/ext.c:6929:42: warning: passing argument 2 of ‘similarity_table_distances’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-12T12:41:47,259 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)))); 2021-07-12T12:41:47,259 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-12T12:41:47,259 In file included from molmod/ext.c:623: 2021-07-12T12:41:47,259 molmod/similarity.h:31:51: note: expected ‘double *’ but argument is of type ‘const double *’ 2021-07-12T12:41:47,260 31 | void similarity_table_distances(size_t n, double *distance_matrix, double *distances_table); 2021-07-12T12:41:47,260 | ~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-12T12:41:47,266 molmod/ext.c: In function ‘__pyx_pf_6molmod_3ext_16similarity_measure’: 2021-07-12T12:41:47,269 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] 2021-07-12T12:41:47,270 7185 | __pyx_t_1 = (((__pyx_v_distances1.shape[0]) != __pyx_v_n1) != 0); 2021-07-12T12:41:47,270 | ^~ 2021-07-12T12:41:47,274 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] 2021-07-12T12:41:47,274 7249 | __pyx_t_1 = (((__pyx_v_distances2.shape[0]) != __pyx_v_n2) != 0); 2021-07-12T12:41:47,274 | ^~ 2021-07-12T12:42:03,408 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 2021-07-12T12:42:03,774 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 2021-07-12T12:42:03,908 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 2021-07-12T12:42:04,066 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 2021-07-12T12:42:04,299 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 2021-07-12T12:42:04,641 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 2021-07-12T12:42:04,861 installing to build/bdist.linux-armv7l/wheel 2021-07-12T12:42:04,861 running install 2021-07-12T12:42:04,862 running install_lib 2021-07-12T12:42:04,866 creating build/bdist.linux-armv7l 2021-07-12T12:42:04,866 creating build/bdist.linux-armv7l/wheel 2021-07-12T12:42:04,869 creating build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,870 copying build/lib.linux-armv7l-3.9/molmod/graphs.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,872 copying build/lib.linux-armv7l-3.9/molmod/log.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,874 copying build/lib.linux-armv7l-3.9/molmod/vectors.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,876 copying build/lib.linux-armv7l-3.9/molmod/ff.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,879 creating build/bdist.linux-armv7l/wheel/molmod/examples 2021-07-12T12:42:04,880 creating build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:04,881 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/d_symmetries.py -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:04,883 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/c_distances.py -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:04,885 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/caffeine.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:04,887 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/ethanol.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:04,889 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/b_neighbors.py -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:04,891 copying build/lib.linux-armv7l-3.9/molmod/examples/002_graphs/a_graphs.py -> build/bdist.linux-armv7l/wheel/molmod/examples/002_graphs 2021-07-12T12:42:04,893 creating build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:04,894 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/dopamine.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:04,896 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/mfi_fragment.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:04,899 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/a_propane_types.py -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:04,901 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/propane.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:04,903 copying build/lib.linux-armv7l-3.9/molmod/examples/004_patterns/b_dopamine_types.py -> build/bdist.linux-armv7l/wheel/molmod/examples/004_patterns 2021-07-12T12:42:04,905 creating build/bdist.linux-armv7l/wheel/molmod/examples/000_units 2021-07-12T12:42:04,906 copying build/lib.linux-armv7l-3.9/molmod/examples/000_units/c_h2rot.py -> build/bdist.linux-armv7l/wheel/molmod/examples/000_units 2021-07-12T12:42:04,908 copying build/lib.linux-armv7l-3.9/molmod/examples/000_units/b_chbond.py -> build/bdist.linux-armv7l/wheel/molmod/examples/000_units 2021-07-12T12:42:04,910 copying build/lib.linux-armv7l-3.9/molmod/examples/000_units/a_reaction.py -> build/bdist.linux-armv7l/wheel/molmod/examples/000_units 2021-07-12T12:42:04,912 creating build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:04,913 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/e_shape.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:04,915 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/d_size.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:04,917 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/b_com.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:04,919 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/a_convert.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:04,921 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/ibuprofen.sdf -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:04,923 copying build/lib.linux-armv7l-3.9/molmod/examples/001_molecules/c_carbon.py -> build/bdist.linux-armv7l/wheel/molmod/examples/001_molecules 2021-07-12T12:42:04,926 creating build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:04,927 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/dopamine.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:04,929 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 2021-07-12T12:42:04,932 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 2021-07-12T12:42:04,934 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/dopamine.fchk -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:04,937 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 2021-07-12T12:42:04,939 copying build/lib.linux-armv7l-3.9/molmod/examples/003_internal_coordinates/propane.xyz -> build/bdist.linux-armv7l/wheel/molmod/examples/003_internal_coordinates 2021-07-12T12:42:04,941 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 2021-07-12T12:42:04,944 copying build/lib.linux-armv7l-3.9/molmod/graphs.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,948 copying build/lib.linux-armv7l-3.9/molmod/toyff.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,951 copying build/lib.linux-armv7l-3.9/molmod/ic.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,954 copying build/lib.linux-armv7l-3.9/molmod/version.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,956 copying build/lib.linux-armv7l-3.9/molmod/unit_cells.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,958 copying build/lib.linux-armv7l-3.9/molmod/similarity.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,960 copying build/lib.linux-armv7l-3.9/molmod/graphs.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,963 copying build/lib.linux-armv7l-3.9/molmod/clusters.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,965 copying build/lib.linux-armv7l-3.9/molmod/molecules.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,967 copying build/lib.linux-armv7l-3.9/molmod/molecules.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,969 copying build/lib.linux-armv7l-3.9/molmod/utils.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,971 copying build/lib.linux-armv7l-3.9/molmod/__init__.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,973 copying build/lib.linux-armv7l-3.9/molmod/pairff.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,976 copying build/lib.linux-armv7l-3.9/molmod/ext.pyx -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,979 copying build/lib.linux-armv7l-3.9/molmod/common.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,981 copying build/lib.linux-armv7l-3.9/molmod/graphs.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,982 copying build/lib.linux-armv7l-3.9/molmod/minimizer.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,986 copying build/lib.linux-armv7l-3.9/molmod/ff.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,988 copying build/lib.linux-armv7l-3.9/molmod/unit_cells.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,991 copying build/lib.linux-armv7l-3.9/molmod/ff.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,993 copying build/lib.linux-armv7l-3.9/molmod/molecular_graphs.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,996 copying build/lib.linux-armv7l-3.9/molmod/similarity.c -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:04,998 copying build/lib.linux-armv7l-3.9/molmod/bonds.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,000 copying build/lib.linux-armv7l-3.9/molmod/symmetry.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,002 copying build/lib.linux-armv7l-3.9/molmod/periodic.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,004 copying build/lib.linux-armv7l-3.9/molmod/isotopes.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,007 copying build/lib.linux-armv7l-3.9/molmod/unit_cells.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,010 creating build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:05,011 copying build/lib.linux-armv7l-3.9/molmod/data/periodic.csv -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:05,014 copying build/lib.linux-armv7l-3.9/molmod/data/periodic.ods -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:05,017 copying build/lib.linux-armv7l-3.9/molmod/data/bonds.ods -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:05,020 copying build/lib.linux-armv7l-3.9/molmod/data/toyff_angles.txt -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:05,024 copying build/lib.linux-armv7l-3.9/molmod/data/bonds.csv -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:05,026 copying build/lib.linux-armv7l-3.9/molmod/data/mass.mas03 -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:05,039 copying build/lib.linux-armv7l-3.9/molmod/data/nubtab03.asc -> build/bdist.linux-armv7l/wheel/molmod/data 2021-07-12T12:42:05,060 creating build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,061 copying build/lib.linux-armv7l-3.9/molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,062 copying build/lib.linux-armv7l-3.9/molmod/data/test/precursor.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,065 copying build/lib.linux-armv7l-3.9/molmod/data/test/cyclopentane.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,066 copying build/lib.linux-armv7l-3.9/molmod/data/test/crystal_api.out -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,078 copying build/lib.linux-armv7l-3.9/molmod/data/test/dlpoly_OUTPUT -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,081 copying build/lib.linux-armv7l-3.9/molmod/data/test/h3zrosihohosioh3.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,083 copying build/lib.linux-armv7l-3.9/molmod/data/test/opt_5ring12T.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,085 copying build/lib.linux-armv7l-3.9/molmod/data/test/alanine.cube -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,088 copying build/lib.linux-armv7l-3.9/molmod/data/test/formol.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,090 copying build/lib.linux-armv7l-3.9/molmod/data/test/dopamine.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,092 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_41893278.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,094 copying build/lib.linux-armv7l-3.9/molmod/data/test/opt_6ring.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,096 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_31646548.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,098 copying build/lib.linux-armv7l-3.9/molmod/data/test/1LJL_Cys10.cml -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,102 copying build/lib.linux-armv7l-3.9/molmod/data/test/dinitrogen.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,103 copying build/lib.linux-armv7l-3.9/molmod/data/test/tpa.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,105 copying build/lib.linux-armv7l-3.9/molmod/data/test/ethane.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,107 copying build/lib.linux-armv7l-3.9/molmod/data/test/example.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,110 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_41893280.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,112 copying build/lib.linux-armv7l-3.9/molmod/data/test/water_md.inp -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,114 copying build/lib.linux-armv7l-3.9/molmod/data/test/dlpoly_HISTORY_an2 -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,116 copying build/lib.linux-armv7l-3.9/molmod/data/test/il2.pdb -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,123 copying build/lib.linux-armv7l-3.9/molmod/data/test/pentapeptide.psf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,126 copying build/lib.linux-armv7l-3.9/molmod/data/test/funny.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,128 copying build/lib.linux-armv7l-3.9/molmod/data/test/dlpoly_HISTORY -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,130 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_40363570.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,132 copying build/lib.linux-armv7l-3.9/molmod/data/test/thf_single.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,134 copying build/lib.linux-armv7l-3.9/molmod/data/test/water.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,136 copying build/lib.linux-armv7l-3.9/molmod/data/test/lau.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,138 copying build/lib.linux-armv7l-3.9/molmod/data/test/oh3siozroh3.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,140 copying build/lib.linux-armv7l-3.9/molmod/data/test/opt_6_6ring.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,142 copying build/lib.linux-armv7l-3.9/molmod/data/test/lammps_dump.txt -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,144 copying build/lib.linux-armv7l-3.9/molmod/data/test/opt_5ring10T.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,146 copying build/lib.linux-armv7l-3.9/molmod/data/test/zr4o8-3.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,148 copying build/lib.linux-armv7l-3.9/molmod/data/test/CID_22898828.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,150 copying build/lib.linux-armv7l-3.9/molmod/data/test/caplayer.cml -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,153 copying build/lib.linux-armv7l-3.9/molmod/data/test/ethene_ethyl_trans.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,155 copying build/lib.linux-armv7l-3.9/molmod/data/test/water2.gro -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,157 copying build/lib.linux-armv7l-3.9/molmod/data/test/butane.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,159 copying build/lib.linux-armv7l-3.9/molmod/data/test/thf.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,163 copying build/lib.linux-armv7l-3.9/molmod/data/test/TRAJECTORY_H2_CPMD -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,165 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_40363571.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,168 copying build/lib.linux-armv7l-3.9/molmod/data/test/thf.psf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,174 copying build/lib.linux-armv7l-3.9/molmod/data/test/thf_64.cell -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,176 copying build/lib.linux-armv7l-3.9/molmod/data/test/octane.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,178 copying build/lib.linux-armv7l-3.9/molmod/data/test/1TOH.b3lyp.fchk -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,193 copying build/lib.linux-armv7l-3.9/molmod/data/test/tea.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,195 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_55127927.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,197 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_56274343.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,199 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_54258192.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,201 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_31646545.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,203 copying build/lib.linux-armv7l-3.9/molmod/data/test/1TOH.b3lyp.trim.fchk -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,205 copying build/lib.linux-armv7l-3.9/molmod/data/test/SID_55488598.sdf -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,207 copying build/lib.linux-armv7l-3.9/molmod/data/test/ethene.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,209 copying build/lib.linux-armv7l-3.9/molmod/data/test/bartek.atrj -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,220 copying build/lib.linux-armv7l-3.9/molmod/data/test/benzene.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,222 copying build/lib.linux-armv7l-3.9/molmod/data/test/argon.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,224 copying build/lib.linux-armv7l-3.9/molmod/data/test/PCGamess_PUNCH -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,258 copying build/lib.linux-armv7l-3.9/molmod/data/test/tetra.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,260 copying build/lib.linux-armv7l-3.9/molmod/data/test/5ringOH.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,262 copying build/lib.linux-armv7l-3.9/molmod/data/test/probes.xyz -> build/bdist.linux-armv7l/wheel/molmod/data/test 2021-07-12T12:42:05,263 copying build/lib.linux-armv7l-3.9/molmod/units.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,265 copying build/lib.linux-armv7l-3.9/molmod/zmatrix.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,268 copying build/lib.linux-armv7l-3.9/molmod/molecules.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,270 copying build/lib.linux-armv7l-3.9/molmod/unit_cells.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,272 copying build/lib.linux-armv7l-3.9/molmod/similarity.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,274 copying build/lib.linux-armv7l-3.9/molmod/molecules.pxd -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,276 copying build/lib.linux-armv7l-3.9/molmod/binning.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,279 copying build/lib.linux-armv7l-3.9/molmod/quaternions.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,282 creating build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,283 copying build/lib.linux-armv7l-3.9/molmod/io/cp2k.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,285 copying build/lib.linux-armv7l-3.9/molmod/io/gromacs.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,288 copying build/lib.linux-armv7l-3.9/molmod/io/chk.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,290 copying build/lib.linux-armv7l-3.9/molmod/io/pdb.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,293 copying build/lib.linux-armv7l-3.9/molmod/io/dlpoly.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,295 copying build/lib.linux-armv7l-3.9/molmod/io/fchk.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,298 copying build/lib.linux-armv7l-3.9/molmod/io/xyz.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,301 copying build/lib.linux-armv7l-3.9/molmod/io/__init__.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,303 copying build/lib.linux-armv7l-3.9/molmod/io/common.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,305 copying build/lib.linux-armv7l-3.9/molmod/io/lammps.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,308 copying build/lib.linux-armv7l-3.9/molmod/io/cml.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,311 copying build/lib.linux-armv7l-3.9/molmod/io/cpmd.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,313 copying build/lib.linux-armv7l-3.9/molmod/io/crystal.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,315 copying build/lib.linux-armv7l-3.9/molmod/io/atrj.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,317 copying build/lib.linux-armv7l-3.9/molmod/io/gamess.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,320 copying build/lib.linux-armv7l-3.9/molmod/io/number_state.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,323 copying build/lib.linux-armv7l-3.9/molmod/io/psf.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,326 creating build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,327 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_crystal.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,330 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_pdb.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,332 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_xyz.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,335 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_dlpoly.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,337 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_sdf.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,339 copying build/lib.linux-armv7l-3.9/molmod/io/test/__init__.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,340 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_cube.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,343 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_number_state.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,345 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_cp2k.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,347 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_lammps.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,349 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_gromacs.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,351 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_gamess.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,353 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_cpmd.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,355 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_psf.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,357 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_fchk.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,359 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_atrj.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,361 copying build/lib.linux-armv7l-3.9/molmod/io/test/test_cml.py -> build/bdist.linux-armv7l/wheel/molmod/io/test 2021-07-12T12:42:05,364 copying build/lib.linux-armv7l-3.9/molmod/io/cube.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,366 copying build/lib.linux-armv7l-3.9/molmod/io/sdf.py -> build/bdist.linux-armv7l/wheel/molmod/io 2021-07-12T12:42:05,369 copying build/lib.linux-armv7l-3.9/molmod/common.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,371 copying build/lib.linux-armv7l-3.9/molmod/ext.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,400 copying build/lib.linux-armv7l-3.9/molmod/similarity.h -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,402 copying build/lib.linux-armv7l-3.9/molmod/randomize.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,405 copying build/lib.linux-armv7l-3.9/molmod/constants.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,408 creating build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,409 copying build/lib.linux-armv7l-3.9/molmod/test/test_transformations.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,411 copying build/lib.linux-armv7l-3.9/molmod/test/test_graphs.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,414 copying build/lib.linux-armv7l-3.9/molmod/test/test_examples.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,417 copying build/lib.linux-armv7l-3.9/molmod/test/test_minimizer.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,419 copying build/lib.linux-armv7l-3.9/molmod/test/test_randomize.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,422 copying build/lib.linux-armv7l-3.9/molmod/test/test_clusters.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,424 copying build/lib.linux-armv7l-3.9/molmod/test/test_data.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,426 copying build/lib.linux-armv7l-3.9/molmod/test/test_quaternions.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,428 copying build/lib.linux-armv7l-3.9/molmod/test/test_similarity.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,431 copying build/lib.linux-armv7l-3.9/molmod/test/__init__.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,433 copying build/lib.linux-armv7l-3.9/molmod/test/common.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,435 copying build/lib.linux-armv7l-3.9/molmod/test/test_unit_cells.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,438 copying build/lib.linux-armv7l-3.9/molmod/test/test_ic.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,440 copying build/lib.linux-armv7l-3.9/molmod/test/test_binning.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,443 copying build/lib.linux-armv7l-3.9/molmod/test/test_molecular_graphs.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,446 copying build/lib.linux-armv7l-3.9/molmod/test/test_symmetry.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,449 copying build/lib.linux-armv7l-3.9/molmod/test/test_units.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,451 copying build/lib.linux-armv7l-3.9/molmod/test/test_log.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,453 copying build/lib.linux-armv7l-3.9/molmod/test/test_pairff.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,455 copying build/lib.linux-armv7l-3.9/molmod/test/test_zmatrix.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,458 copying build/lib.linux-armv7l-3.9/molmod/test/test_toyff.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,461 copying build/lib.linux-armv7l-3.9/molmod/test/test_molecules.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,463 copying build/lib.linux-armv7l-3.9/molmod/test/test_vectors.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,465 copying build/lib.linux-armv7l-3.9/molmod/test/test_utils.py -> build/bdist.linux-armv7l/wheel/molmod/test 2021-07-12T12:42:05,467 copying build/lib.linux-armv7l-3.9/molmod/transformations.py -> build/bdist.linux-armv7l/wheel/molmod 2021-07-12T12:42:05,470 running install_egg_info 2021-07-12T12:42:05,476 Copying molmod.egg-info to build/bdist.linux-armv7l/wheel/molmod-1.3.2-py3.9.egg-info 2021-07-12T12:42:05,489 running install_scripts 2021-07-12T12:42:05,531 adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*") 2021-07-12T12:42:05,537 creating build/bdist.linux-armv7l/wheel/molmod-1.3.2.dist-info/WHEEL 2021-07-12T12:42:05,540 creating '/tmp/pip-wheel-aiu3ubwh/molmod-1.3.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-12T12:42:05,544 adding 'molmod/__init__.py' 2021-07-12T12:42:05,546 adding 'molmod/binning.py' 2021-07-12T12:42:05,548 adding 'molmod/bonds.py' 2021-07-12T12:42:05,549 adding 'molmod/clusters.py' 2021-07-12T12:42:05,551 adding 'molmod/common.c' 2021-07-12T12:42:05,552 adding 'molmod/common.h' 2021-07-12T12:42:05,554 adding 'molmod/constants.py' 2021-07-12T12:42:05,778 adding 'molmod/ext.cpython-39-arm-linux-gnueabihf.so' 2021-07-12T12:42:05,789 adding 'molmod/ext.pyx' 2021-07-12T12:42:05,790 adding 'molmod/ff.c' 2021-07-12T12:42:05,792 adding 'molmod/ff.h' 2021-07-12T12:42:05,793 adding 'molmod/ff.pxd' 2021-07-12T12:42:05,794 adding 'molmod/graphs.c' 2021-07-12T12:42:05,795 adding 'molmod/graphs.h' 2021-07-12T12:42:05,796 adding 'molmod/graphs.pxd' 2021-07-12T12:42:05,805 adding 'molmod/graphs.py' 2021-07-12T12:42:05,809 adding 'molmod/ic.py' 2021-07-12T12:42:05,811 adding 'molmod/isotopes.py' 2021-07-12T12:42:05,813 adding 'molmod/log.py' 2021-07-12T12:42:05,822 adding 'molmod/minimizer.py' 2021-07-12T12:42:05,826 adding 'molmod/molecular_graphs.py' 2021-07-12T12:42:05,827 adding 'molmod/molecules.c' 2021-07-12T12:42:05,828 adding 'molmod/molecules.h' 2021-07-12T12:42:05,830 adding 'molmod/molecules.pxd' 2021-07-12T12:42:05,832 adding 'molmod/molecules.py' 2021-07-12T12:42:05,834 adding 'molmod/pairff.py' 2021-07-12T12:42:05,835 adding 'molmod/periodic.py' 2021-07-12T12:42:05,837 adding 'molmod/quaternions.py' 2021-07-12T12:42:05,840 adding 'molmod/randomize.py' 2021-07-12T12:42:05,841 adding 'molmod/similarity.c' 2021-07-12T12:42:05,842 adding 'molmod/similarity.h' 2021-07-12T12:42:05,844 adding 'molmod/similarity.pxd' 2021-07-12T12:42:05,845 adding 'molmod/similarity.py' 2021-07-12T12:42:05,847 adding 'molmod/symmetry.py' 2021-07-12T12:42:05,849 adding 'molmod/toyff.py' 2021-07-12T12:42:05,851 adding 'molmod/transformations.py' 2021-07-12T12:42:05,853 adding 'molmod/unit_cells.c' 2021-07-12T12:42:05,854 adding 'molmod/unit_cells.h' 2021-07-12T12:42:05,856 adding 'molmod/unit_cells.pxd' 2021-07-12T12:42:05,858 adding 'molmod/unit_cells.py' 2021-07-12T12:42:05,860 adding 'molmod/units.py' 2021-07-12T12:42:05,862 adding 'molmod/utils.py' 2021-07-12T12:42:05,864 adding 'molmod/vectors.py' 2021-07-12T12:42:05,865 adding 'molmod/version.py' 2021-07-12T12:42:05,866 adding 'molmod/zmatrix.py' 2021-07-12T12:42:05,869 adding 'molmod/data/bonds.csv' 2021-07-12T12:42:05,871 adding 'molmod/data/bonds.ods' 2021-07-12T12:42:05,954 adding 'molmod/data/mass.mas03' 2021-07-12T12:42:06,036 adding 'molmod/data/nubtab03.asc' 2021-07-12T12:42:06,043 adding 'molmod/data/periodic.csv' 2021-07-12T12:42:06,046 adding 'molmod/data/periodic.ods' 2021-07-12T12:42:06,061 adding 'molmod/data/toyff_angles.txt' 2021-07-12T12:42:06,068 adding 'molmod/data/test/1LJL_Cys10.cml' 2021-07-12T12:42:06,199 adding 'molmod/data/test/1TOH.b3lyp.fchk' 2021-07-12T12:42:06,205 adding 'molmod/data/test/1TOH.b3lyp.trim.fchk' 2021-07-12T12:42:06,206 adding 'molmod/data/test/5ringOH.xyz' 2021-07-12T12:42:06,207 adding 'molmod/data/test/CID_22898828.sdf' 2021-07-12T12:42:06,452 adding 'molmod/data/test/PCGamess_PUNCH' 2021-07-12T12:42:06,461 adding 'molmod/data/test/SID_31646545.sdf' 2021-07-12T12:42:06,462 adding 'molmod/data/test/SID_31646548.sdf' 2021-07-12T12:42:06,464 adding 'molmod/data/test/SID_40363570.sdf' 2021-07-12T12:42:06,465 adding 'molmod/data/test/SID_40363571.sdf' 2021-07-12T12:42:06,466 adding 'molmod/data/test/SID_41893278.sdf' 2021-07-12T12:42:06,468 adding 'molmod/data/test/SID_41893280.sdf' 2021-07-12T12:42:06,469 adding 'molmod/data/test/SID_54258192.sdf' 2021-07-12T12:42:06,470 adding 'molmod/data/test/SID_55127927.sdf' 2021-07-12T12:42:06,471 adding 'molmod/data/test/SID_55488598.sdf' 2021-07-12T12:42:06,473 adding 'molmod/data/test/SID_56274343.sdf' 2021-07-12T12:42:06,474 adding 'molmod/data/test/TRAJECTORY_H2_CPMD' 2021-07-12T12:42:06,478 adding 'molmod/data/test/alanine.cube' 2021-07-12T12:42:06,479 adding 'molmod/data/test/argon.xyz' 2021-07-12T12:42:06,557 adding 'molmod/data/test/bartek.atrj' 2021-07-12T12:42:06,561 adding 'molmod/data/test/benzene.xyz' 2021-07-12T12:42:06,562 adding 'molmod/data/test/butane.xyz' 2021-07-12T12:42:06,564 adding 'molmod/data/test/caplayer.cml' 2021-07-12T12:42:06,632 adding 'molmod/data/test/crystal_api.out' 2021-07-12T12:42:06,637 adding 'molmod/data/test/cyclopentane.xyz' 2021-07-12T12:42:06,638 adding 'molmod/data/test/dinitrogen.xyz' 2021-07-12T12:42:06,639 adding 'molmod/data/test/dlpoly_HISTORY' 2021-07-12T12:42:06,641 adding 'molmod/data/test/dlpoly_HISTORY_an2' 2021-07-12T12:42:06,646 adding 'molmod/data/test/dlpoly_OUTPUT' 2021-07-12T12:42:06,647 adding 'molmod/data/test/dopamine.xyz' 2021-07-12T12:42:06,648 adding 'molmod/data/test/ethane.xyz' 2021-07-12T12:42:06,649 adding 'molmod/data/test/ethene.xyz' 2021-07-12T12:42:06,651 adding 'molmod/data/test/ethene_ethyl_trans.xyz' 2021-07-12T12:42:06,652 adding 'molmod/data/test/example.sdf' 2021-07-12T12:42:06,653 adding 'molmod/data/test/formol.xyz' 2021-07-12T12:42:06,654 adding 'molmod/data/test/funny.xyz' 2021-07-12T12:42:06,655 adding 'molmod/data/test/h3zrosihohosioh3.xyz' 2021-07-12T12:42:06,686 adding 'molmod/data/test/il2.pdb' 2021-07-12T12:42:06,690 adding 'molmod/data/test/lammps_dump.txt' 2021-07-12T12:42:06,691 adding 'molmod/data/test/lau.xyz' 2021-07-12T12:42:06,692 adding 'molmod/data/test/octane.xyz' 2021-07-12T12:42:06,693 adding 'molmod/data/test/oh3siozroh3.xyz' 2021-07-12T12:42:06,695 adding 'molmod/data/test/opt_5ring10T.xyz' 2021-07-12T12:42:06,696 adding 'molmod/data/test/opt_5ring12T.xyz' 2021-07-12T12:42:06,697 adding 'molmod/data/test/opt_6_6ring.xyz' 2021-07-12T12:42:06,699 adding 'molmod/data/test/opt_6ring.xyz' 2021-07-12T12:42:06,700 adding 'molmod/data/test/osih2osihosih2osih2ozrh2oh.xyz' 2021-07-12T12:42:06,702 adding 'molmod/data/test/pentapeptide.psf' 2021-07-12T12:42:06,704 adding 'molmod/data/test/precursor.xyz' 2021-07-12T12:42:06,705 adding 'molmod/data/test/probes.xyz' 2021-07-12T12:42:06,706 adding 'molmod/data/test/tea.xyz' 2021-07-12T12:42:06,707 adding 'molmod/data/test/tetra.xyz' 2021-07-12T12:42:06,729 adding 'molmod/data/test/thf.psf' 2021-07-12T12:42:06,736 adding 'molmod/data/test/thf.xyz' 2021-07-12T12:42:06,738 adding 'molmod/data/test/thf_64.cell' 2021-07-12T12:42:06,739 adding 'molmod/data/test/thf_single.xyz' 2021-07-12T12:42:06,741 adding 'molmod/data/test/tpa.xyz' 2021-07-12T12:42:06,742 adding 'molmod/data/test/water.xyz' 2021-07-12T12:42:06,743 adding 'molmod/data/test/water2.gro' 2021-07-12T12:42:06,744 adding 'molmod/data/test/water_md.inp' 2021-07-12T12:42:06,745 adding 'molmod/data/test/zr4o8-3.xyz' 2021-07-12T12:42:06,747 adding 'molmod/examples/000_units/a_reaction.py' 2021-07-12T12:42:06,749 adding 'molmod/examples/000_units/b_chbond.py' 2021-07-12T12:42:06,750 adding 'molmod/examples/000_units/c_h2rot.py' 2021-07-12T12:42:06,752 adding 'molmod/examples/001_molecules/a_convert.py' 2021-07-12T12:42:06,753 adding 'molmod/examples/001_molecules/b_com.py' 2021-07-12T12:42:06,754 adding 'molmod/examples/001_molecules/c_carbon.py' 2021-07-12T12:42:06,755 adding 'molmod/examples/001_molecules/d_size.py' 2021-07-12T12:42:06,757 adding 'molmod/examples/001_molecules/e_shape.py' 2021-07-12T12:42:06,758 adding 'molmod/examples/001_molecules/ibuprofen.sdf' 2021-07-12T12:42:06,760 adding 'molmod/examples/002_graphs/a_graphs.py' 2021-07-12T12:42:06,762 adding 'molmod/examples/002_graphs/b_neighbors.py' 2021-07-12T12:42:06,763 adding 'molmod/examples/002_graphs/c_distances.py' 2021-07-12T12:42:06,764 adding 'molmod/examples/002_graphs/caffeine.xyz' 2021-07-12T12:42:06,765 adding 'molmod/examples/002_graphs/d_symmetries.py' 2021-07-12T12:42:06,766 adding 'molmod/examples/002_graphs/ethanol.xyz' 2021-07-12T12:42:06,768 adding 'molmod/examples/003_internal_coordinates/a_bond_length.py' 2021-07-12T12:42:06,770 adding 'molmod/examples/003_internal_coordinates/b_bending_angles.py' 2021-07-12T12:42:06,771 adding 'molmod/examples/003_internal_coordinates/c_ff_hessian.py' 2021-07-12T12:42:06,773 adding 'molmod/examples/003_internal_coordinates/d_dft_hessian.py' 2021-07-12T12:42:06,783 adding 'molmod/examples/003_internal_coordinates/dopamine.fchk' 2021-07-12T12:42:06,785 adding 'molmod/examples/003_internal_coordinates/dopamine.xyz' 2021-07-12T12:42:06,786 adding 'molmod/examples/003_internal_coordinates/propane.xyz' 2021-07-12T12:42:06,788 adding 'molmod/examples/004_patterns/a_propane_types.py' 2021-07-12T12:42:06,790 adding 'molmod/examples/004_patterns/b_dopamine_types.py' 2021-07-12T12:42:06,791 adding 'molmod/examples/004_patterns/dopamine.xyz' 2021-07-12T12:42:06,792 adding 'molmod/examples/004_patterns/mfi_fragment.xyz' 2021-07-12T12:42:06,794 adding 'molmod/examples/004_patterns/propane.xyz' 2021-07-12T12:42:06,796 adding 'molmod/io/__init__.py' 2021-07-12T12:42:06,797 adding 'molmod/io/atrj.py' 2021-07-12T12:42:06,799 adding 'molmod/io/chk.py' 2021-07-12T12:42:06,801 adding 'molmod/io/cml.py' 2021-07-12T12:42:06,802 adding 'molmod/io/common.py' 2021-07-12T12:42:06,804 adding 'molmod/io/cp2k.py' 2021-07-12T12:42:06,806 adding 'molmod/io/cpmd.py' 2021-07-12T12:42:06,807 adding 'molmod/io/crystal.py' 2021-07-12T12:42:06,809 adding 'molmod/io/cube.py' 2021-07-12T12:42:06,811 adding 'molmod/io/dlpoly.py' 2021-07-12T12:42:06,813 adding 'molmod/io/fchk.py' 2021-07-12T12:42:06,815 adding 'molmod/io/gamess.py' 2021-07-12T12:42:06,816 adding 'molmod/io/gromacs.py' 2021-07-12T12:42:06,818 adding 'molmod/io/lammps.py' 2021-07-12T12:42:06,820 adding 'molmod/io/number_state.py' 2021-07-12T12:42:06,822 adding 'molmod/io/pdb.py' 2021-07-12T12:42:06,824 adding 'molmod/io/psf.py' 2021-07-12T12:42:06,826 adding 'molmod/io/sdf.py' 2021-07-12T12:42:06,827 adding 'molmod/io/xyz.py' 2021-07-12T12:42:06,830 adding 'molmod/io/test/__init__.py' 2021-07-12T12:42:06,831 adding 'molmod/io/test/test_atrj.py' 2021-07-12T12:42:06,832 adding 'molmod/io/test/test_cml.py' 2021-07-12T12:42:06,834 adding 'molmod/io/test/test_cp2k.py' 2021-07-12T12:42:06,835 adding 'molmod/io/test/test_cpmd.py' 2021-07-12T12:42:06,836 adding 'molmod/io/test/test_crystal.py' 2021-07-12T12:42:06,838 adding 'molmod/io/test/test_cube.py' 2021-07-12T12:42:06,840 adding 'molmod/io/test/test_dlpoly.py' 2021-07-12T12:42:06,841 adding 'molmod/io/test/test_fchk.py' 2021-07-12T12:42:06,842 adding 'molmod/io/test/test_gamess.py' 2021-07-12T12:42:06,843 adding 'molmod/io/test/test_gromacs.py' 2021-07-12T12:42:06,845 adding 'molmod/io/test/test_lammps.py' 2021-07-12T12:42:06,846 adding 'molmod/io/test/test_number_state.py' 2021-07-12T12:42:06,847 adding 'molmod/io/test/test_pdb.py' 2021-07-12T12:42:06,849 adding 'molmod/io/test/test_psf.py' 2021-07-12T12:42:06,850 adding 'molmod/io/test/test_sdf.py' 2021-07-12T12:42:06,851 adding 'molmod/io/test/test_xyz.py' 2021-07-12T12:42:06,854 adding 'molmod/test/__init__.py' 2021-07-12T12:42:06,855 adding 'molmod/test/common.py' 2021-07-12T12:42:06,857 adding 'molmod/test/test_binning.py' 2021-07-12T12:42:06,858 adding 'molmod/test/test_clusters.py' 2021-07-12T12:42:06,860 adding 'molmod/test/test_data.py' 2021-07-12T12:42:06,861 adding 'molmod/test/test_examples.py' 2021-07-12T12:42:06,864 adding 'molmod/test/test_graphs.py' 2021-07-12T12:42:06,866 adding 'molmod/test/test_ic.py' 2021-07-12T12:42:06,867 adding 'molmod/test/test_log.py' 2021-07-12T12:42:06,869 adding 'molmod/test/test_minimizer.py' 2021-07-12T12:42:06,872 adding 'molmod/test/test_molecular_graphs.py' 2021-07-12T12:42:06,874 adding 'molmod/test/test_molecules.py' 2021-07-12T12:42:06,876 adding 'molmod/test/test_pairff.py' 2021-07-12T12:42:06,878 adding 'molmod/test/test_quaternions.py' 2021-07-12T12:42:06,879 adding 'molmod/test/test_randomize.py' 2021-07-12T12:42:06,881 adding 'molmod/test/test_similarity.py' 2021-07-12T12:42:06,882 adding 'molmod/test/test_symmetry.py' 2021-07-12T12:42:06,883 adding 'molmod/test/test_toyff.py' 2021-07-12T12:42:06,886 adding 'molmod/test/test_transformations.py' 2021-07-12T12:42:06,888 adding 'molmod/test/test_unit_cells.py' 2021-07-12T12:42:06,890 adding 'molmod/test/test_units.py' 2021-07-12T12:42:06,891 adding 'molmod/test/test_utils.py' 2021-07-12T12:42:06,892 adding 'molmod/test/test_vectors.py' 2021-07-12T12:42:06,894 adding 'molmod/test/test_zmatrix.py' 2021-07-12T12:42:06,901 adding 'molmod-1.3.2.dist-info/LICENSE.txt' 2021-07-12T12:42:06,903 adding 'molmod-1.3.2.dist-info/METADATA' 2021-07-12T12:42:06,904 adding 'molmod-1.3.2.dist-info/WHEEL' 2021-07-12T12:42:06,904 adding 'molmod-1.3.2.dist-info/top_level.txt' 2021-07-12T12:42:06,908 adding 'molmod-1.3.2.dist-info/RECORD' 2021-07-12T12:42:06,939 removing build/bdist.linux-armv7l/wheel 2021-07-12T12:42:07,383 Building wheel for molmod (setup.py): finished with status 'done' 2021-07-12T12:42:07,410 Created wheel for molmod: filename=molmod-1.3.2-cp39-cp39-linux_armv7l.whl size=1953944 sha256=f37c6d241bdfee045f443a9d55f9509d86d894a0c11e09ad4c38c91d235649c7 2021-07-12T12:42:07,410 Stored in directory: /tmp/pip-ephem-wheel-cache-jbg47v5j/wheels/7a/16/54/c3a191305c69fcac3e64b096ac1b3ba1d55812021a384690f3 2021-07-12T12:42:07,427 Successfully built molmod 2021-07-12T12:42:07,500 Removed build tracker: '/tmp/pip-req-tracker-l4jtce6j'