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2021-07-09T21:00:54,805 Found link https://files.pythonhosted.org/packages/78/ae/82df7eca71fa9e71ad4638f8c222164ccc3583874cb4a6875a04586312bc/mdtraj-1.5.1.zip#sha256=d97591eebf1e9ae04c2b2e144340a959ed359fe33037c647b174f017bab482c3 (from https://pypi.org/simple/mdtraj/), version: 1.5.1 2021-07-09T21:00:54,805 Found link https://files.pythonhosted.org/packages/40/21/40aeb64c81f480e07b1e1c31c6b3b332bc38df08d5fd30210fc235acdb3d/mdtraj-1.6.0.tar.gz#sha256=6da885f0f3bad7baa27adf6f7cac62282e02e58b319144f1fefeaa6d3ca8fe7a (from https://pypi.org/simple/mdtraj/), version: 1.6.0 2021-07-09T21:00:54,805 Found link https://files.pythonhosted.org/packages/8f/9e/cf5814ce6a29a474dc2b61492ed36dde1397b1707e63248bafe495529c29/mdtraj-1.6.0.zip#sha256=9d281e43cbc7133615dc0b81e63f64e79e39e3d25098103798301f3c06383c0b (from https://pypi.org/simple/mdtraj/), version: 1.6.0 2021-07-09T21:00:54,806 Found link https://files.pythonhosted.org/packages/a7/09/abb145901e09665d3a7931527e34a160049cebf4eba3506a69db2093f5f9/mdtraj-1.6.1.tar.gz#sha256=1d390acb7bbe09c7a2b1c639c641c47eef09c37bd525cd83c201addda37074c8 (from https://pypi.org/simple/mdtraj/), version: 1.6.1 2021-07-09T21:00:54,806 Found link https://files.pythonhosted.org/packages/38/44/179f101e32ab7ceb52864fb4ef2955c0807b9f548c087f39f2cfd18cb498/mdtraj-1.6.1.zip#sha256=bca98c6339d04b36934b37857eae9f42fb667e1745d4d7dc29ebfd4e3c653365 (from https://pypi.org/simple/mdtraj/), version: 1.6.1 2021-07-09T21:00:54,806 Found link https://files.pythonhosted.org/packages/bf/81/6f611041374bd7d2d49a15040d999cc52eed1a44e856a4a8d9c02370ac37/mdtraj-1.7.2.tar.gz#sha256=1bc9fb06e84f6562e51e040946dae0b940eaca4760f78f3ac451f4a89b132a9a (from https://pypi.org/simple/mdtraj/), version: 1.7.2 2021-07-09T21:00:54,806 Found link https://files.pythonhosted.org/packages/ff/b2/8785a8c9c7119e1a7c4e64072ccf428f75a3b0a9782a7ac25e5402b0a59d/mdtraj-1.7.2.zip#sha256=3158176cd2c21d2abdff5b2cbd9cac323f337b831123d5201bbb7d3fbe69e714 (from https://pypi.org/simple/mdtraj/), version: 1.7.2 2021-07-09T21:00:54,807 Found link https://files.pythonhosted.org/packages/cd/9f/027fa58d4e93dd3d700e22d5766961c970f6882c2bffd33daef55219d078/mdtraj-1.8.0.tar.gz#sha256=480fa4c280146e91db0ab7811f6fba5da29e89452b071d366a8e68247a88ffea (from https://pypi.org/simple/mdtraj/), version: 1.8.0 2021-07-09T21:00:54,807 Found link https://files.pythonhosted.org/packages/4a/2e/5bb01aaa8cd2ea9d75dd2ac12fd9f04f7137a8c996bde0138ad1b5e54ecb/mdtraj-1.8.0.zip#sha256=867325cb206dca4a605de4877e17e5e1983f2e778a6ef64594bd4250142561a8 (from https://pypi.org/simple/mdtraj/), version: 1.8.0 2021-07-09T21:00:54,807 Found link https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz#sha256=ca1ae07c5f5ce59940a48388ac9b098f8e22743b5f3ed3f46d5e3d1317b06282 (from https://pypi.org/simple/mdtraj/), version: 1.9.1 2021-07-09T21:00:54,808 Found link https://files.pythonhosted.org/packages/e0/9e/857f613eae8af3fb8cc73904b3edf622c58de3884c5989e4466973c3c9ee/mdtraj-1.9.2.tar.gz#sha256=cdd926f19c007955f0f768d36d696f3e77b4c8030289a2b40eb97a91cebacd0f (from https://pypi.org/simple/mdtraj/), version: 1.9.2 2021-07-09T21:00:54,808 Found link https://files.pythonhosted.org/packages/72/68/1efc74927df6fdaaa4816556a2534f4560cb69ed573ccac728e4fb8e3e09/mdtraj-1.9.3.tar.gz#sha256=5d95e045b1dd093a26bf6fea9895c3c6b52955d8f7fceee867a519ccf29640b3 (from https://pypi.org/simple/mdtraj/), version: 1.9.3 2021-07-09T21:00:54,808 Found link https://files.pythonhosted.org/packages/50/1d/581a080a1900f61bb1c0388e29517a54d4034faa094d40d794e1f96597d9/mdtraj-1.9.4.tar.gz#sha256=d5d28be24dd5f38e8b272c3a445a6cdbffc374b30e891c5535f65bb20f7e8b24 (from https://pypi.org/simple/mdtraj/), version: 1.9.4 2021-07-09T21:00:54,809 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/1b/77/3ac1597812fc28964662587d405f85986206192623b434f7d0fa1b4a6a5b/mdtraj-1.9.5-cp36-cp36m-manylinux1_x86_64.whl#sha256=c02a9a589acc98dd3cc4db9b0cb21725f5e2cb9484c14cc4fa032a4663c7a1e9 (from https://pypi.org/simple/mdtraj/) 2021-07-09T21:00:54,809 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/af/da/271e93bb98bc93ccac17bc1f31f814be4f9e7024ac19bf31af892a462030/mdtraj-1.9.5-cp37-cp37m-manylinux1_x86_64.whl#sha256=8816f9a91826e46a413fd1a5ffd663b4076cf4c3b8930bb2046814d1438a88ee (from https://pypi.org/simple/mdtraj/) 2021-07-09T21:00:54,810 Skipping link: none of the wheel's tags (cp38-cp38-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/3b/fd/4ffba665d0b0346072f61d0e8ef7ab281202db445d99136c717c89169a97/mdtraj-1.9.5-cp38-cp38-manylinux1_x86_64.whl#sha256=84bb3ced0ff61c4b3b38a36d71837599f50c8723c5d9e555dced51d0d09e10a1 (from https://pypi.org/simple/mdtraj/) 2021-07-09T21:00:54,810 Skipping link: none of the wheel's tags (cp39-cp39-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/68/53/2f666107565f4735abd859b6af6867353eb08d0e9728d90fb0abc12d578e/mdtraj-1.9.5-cp39-cp39-manylinux1_x86_64.whl#sha256=7eae1adc6aa876396c9797d80db3f71da831601fb1739da731e1de9ca8ac96ab (from https://pypi.org/simple/mdtraj/) 2021-07-09T21:00:54,810 Found link https://files.pythonhosted.org/packages/d8/cb/5dcc31c7e2c4485bd2aea66233def28954f2dc530607f5c43fefab71a963/mdtraj-1.9.5.tar.gz#sha256=f22c28c9dd51aa0f8692078dd3c2c7a338a7ca27cbd9aaeb669a60361e95adc4 (from https://pypi.org/simple/mdtraj/), version: 1.9.5 2021-07-09T21:00:54,811 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64, cp36-cp36m-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/fe/a7/2a1392fe56ddd22a9cf5dcff7d684bdd7ce146d5c32839080dd8de7122dd/mdtraj-1.9.6-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=8d437742ec45ff619c7a50afacf16f3a791d604cd0be74b5b74d90b0dc3f577a (from https://pypi.org/simple/mdtraj/) 2021-07-09T21:00:54,811 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64, cp37-cp37m-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/ce/ee/2015ff88cacb7c75b5e1cf6a57e8a089549b0e76bcd9474a08845f7ef12f/mdtraj-1.9.6-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=49f4251f83a7fdea4a8122369ef47f213bb1c1cfc38b91177e98985484fb63bf (from https://pypi.org/simple/mdtraj/) 2021-07-09T21:00:54,812 Skipping link: none of the wheel's tags (cp38-cp38-manylinux1_x86_64, cp38-cp38-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c0/61/2fb002b9b2ab90567eb1a837ed510152ddadd5b8358ac800b591e37675e0/mdtraj-1.9.6-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=84bf863729d435df0dd1f86c3023cbe85b8940b102f9d6ef6ce00dcb9130883c (from https://pypi.org/simple/mdtraj/) 2021-07-09T21:00:54,812 Skipping link: none of the wheel's tags (cp39-cp39-manylinux1_x86_64, cp39-cp39-manylinux_2_5_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/09/49/85dc22a3c28108dfd0bce8a4268ae3937167b18fac531a0d801505cad7d9/mdtraj-1.9.6-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl#sha256=44fcc435df4057126c123585e36a8a4563e24588ad438c916751e2e01501e2ff (from https://pypi.org/simple/mdtraj/) 2021-07-09T21:00:54,812 Found link https://files.pythonhosted.org/packages/12/72/af80a9be1a0b8086cff7572c72b7a06e917cc128719a70b087e77e23736c/mdtraj-1.9.6.tar.gz#sha256=5b7c9b98dd0a1c1a2ddd6c1690fba6096a63314da2e79e05a8a1402b8949ad3c (from https://pypi.org/simple/mdtraj/), version: 1.9.6 2021-07-09T21:00:54,813 Skipping link: not a file: https://pypi.org/simple/mdtraj/ 2021-07-09T21:00:54,821 Given no hashes to check 2 links for project 'mdtraj': discarding no candidates 2021-07-09T21:00:54,839 Collecting mdtraj==0.8.0 2021-07-09T21:00:54,840 Created temporary directory: /tmp/pip-unpack-zh44oy88 2021-07-09T21:00:56,099 Downloading mdtraj-0.8.0.zip (2.6 MB) 2021-07-09T21:00:57,171 Added mdtraj==0.8.0 from https://files.pythonhosted.org/packages/d8/87/01f61e5cabbf391ed20ec15854454f7bd76d752413be983654c2de738292/mdtraj-0.8.0.zip#sha256=d255f9f0509205109aa08a853fdb004cac9e8075b5ba370d17903519ff7c0f39 to build tracker '/tmp/pip-req-tracker-q6uo47dl' 2021-07-09T21:00:57,172 Running setup.py (path:/tmp/pip-wheel-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/setup.py) egg_info for package mdtraj 2021-07-09T21:00:57,173 Created temporary directory: /tmp/pip-pip-egg-info-ryyepx4q 2021-07-09T21:00:57,173 Running command python setup.py egg_info 2021-07-09T21:00:58,857 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T21:00:58,857 running egg_info 2021-07-09T21:00:58,859 creating /tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info 2021-07-09T21:00:58,860 writing /tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info/PKG-INFO 2021-07-09T21:00:58,862 writing dependency_links to /tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info/dependency_links.txt 2021-07-09T21:00:58,864 writing entry points to /tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info/entry_points.txt 2021-07-09T21:00:58,865 writing requirements to /tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info/requires.txt 2021-07-09T21:00:58,866 writing top-level names to /tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info/top_level.txt 2021-07-09T21:00:58,868 writing manifest file '/tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info/SOURCES.txt' 2021-07-09T21:00:59,036 reading manifest file '/tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info/SOURCES.txt' 2021-07-09T21:00:59,037 reading manifest template 'MANIFEST.in' 2021-07-09T21:00:59,072 writing manifest file '/tmp/pip-pip-egg-info-ryyepx4q/mdtraj.egg-info/SOURCES.txt' 2021-07-09T21:00:59,177 Source in /tmp/pip-wheel-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42 has version 0.8.0, which satisfies requirement mdtraj==0.8.0 from https://files.pythonhosted.org/packages/d8/87/01f61e5cabbf391ed20ec15854454f7bd76d752413be983654c2de738292/mdtraj-0.8.0.zip#sha256=d255f9f0509205109aa08a853fdb004cac9e8075b5ba370d17903519ff7c0f39 2021-07-09T21:00:59,178 Removed mdtraj==0.8.0 from https://files.pythonhosted.org/packages/d8/87/01f61e5cabbf391ed20ec15854454f7bd76d752413be983654c2de738292/mdtraj-0.8.0.zip#sha256=d255f9f0509205109aa08a853fdb004cac9e8075b5ba370d17903519ff7c0f39 from build tracker '/tmp/pip-req-tracker-q6uo47dl' 2021-07-09T21:00:59,182 Created temporary directory: /tmp/pip-unpack-kzd50uzi 2021-07-09T21:00:59,182 Building wheels for collected packages: mdtraj 2021-07-09T21:00:59,186 Created temporary directory: /tmp/pip-wheel-x_gvurb2 2021-07-09T21:00:59,187 Building wheel for mdtraj (setup.py): started 2021-07-09T21:00:59,187 Destination directory: /tmp/pip-wheel-x_gvurb2 2021-07-09T21:00:59,188 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/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-x_gvurb2 2021-07-09T21:01:00,621 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T21:01:00,841 running bdist_wheel 2021-07-09T21:01:00,845 running build 2021-07-09T21:01:00,845 running build_py 2021-07-09T21:01:00,980 creating build 2021-07-09T21:01:00,980 creating build/lib.linux-armv7l-3.9 2021-07-09T21:01:00,981 creating build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T21:01:00,982 creating build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T21:01:00,983 copying scripts/mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T21:01:00,986 copying scripts/mdinspect.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T21:01:00,988 copying scripts/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/scripts 2021-07-09T21:01:00,990 copying MDTraj/version.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T21:01:00,992 copying MDTraj/io.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T21:01:00,995 copying MDTraj/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj 2021-07-09T21:01:00,998 creating build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:00,998 copying MDTraj/tests/test_reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,001 copying MDTraj/tests/test_io.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,003 copying MDTraj/tests/test_mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,005 copying MDTraj/tests/test_trr.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,007 copying MDTraj/tests/test_trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,010 copying MDTraj/tests/test_binpos.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,013 copying MDTraj/tests/test_hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,016 copying MDTraj/tests/test_xtc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,018 copying MDTraj/tests/test_prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,020 copying MDTraj/tests/test_rmsd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,023 copying MDTraj/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,025 copying MDTraj/tests/test_xml.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,027 copying MDTraj/tests/test_topology.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,030 copying MDTraj/tests/test_netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,033 copying MDTraj/tests/test_mdconvert.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,036 copying MDTraj/tests/test_dcd.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,039 copying MDTraj/tests/test_arc.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,041 copying MDTraj/tests/test_lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,044 copying MDTraj/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/tests 2021-07-09T21:01:01,047 creating build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T21:01:01,048 copying MDTraj/utils/six.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T21:01:01,052 copying MDTraj/utils/ffi.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T21:01:01,054 copying MDTraj/utils/delay_import.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T21:01:01,056 copying MDTraj/utils/unitcell.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T21:01:01,059 copying MDTraj/utils/arrays.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T21:01:01,065 copying MDTraj/utils/test.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T21:01:01,068 copying MDTraj/utils/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils 2021-07-09T21:01:01,071 creating build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,072 copying MDTraj/utils/unit/mymatrix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,076 copying MDTraj/utils/unit/unit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,079 copying MDTraj/utils/unit/baseunit.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,082 copying MDTraj/utils/unit/doctests.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,085 copying MDTraj/utils/unit/unit_math.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,088 copying MDTraj/utils/unit/prefix.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,091 copying MDTraj/utils/unit/unit_operators.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,093 copying MDTraj/utils/unit/quantity.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,097 copying MDTraj/utils/unit/constants.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,099 copying MDTraj/utils/unit/basedimension.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,101 copying MDTraj/utils/unit/standard_dimensions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,103 copying MDTraj/utils/unit/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,106 copying MDTraj/utils/unit/unit_definitions.py -> build/lib.linux-armv7l-3.9/mdtraj/utils/unit 2021-07-09T21:01:01,112 creating build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T21:01:01,114 copying MDTraj/testing/testing.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T21:01:01,116 copying MDTraj/testing/docscrape.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T21:01:01,119 copying MDTraj/testing/docstrings.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T21:01:01,122 copying MDTraj/testing/nosetester.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T21:01:01,124 copying MDTraj/testing/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/testing 2021-07-09T21:01:01,127 creating build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T21:01:01,128 copying MDTraj/reporters/netcdfreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T21:01:01,130 copying MDTraj/reporters/hdf5reporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T21:01:01,133 copying MDTraj/reporters/dcdreporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T21:01:01,135 copying MDTraj/reporters/basereporter.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T21:01:01,138 copying MDTraj/reporters/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/reporters 2021-07-09T21:01:01,141 creating build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,142 copying MDTraj/geometry/sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,145 copying MDTraj/geometry/rg.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,147 copying MDTraj/geometry/distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,149 copying MDTraj/geometry/angle.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,152 copying MDTraj/geometry/contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,154 copying MDTraj/geometry/internal.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,157 copying MDTraj/geometry/hbond.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,160 copying MDTraj/geometry/dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,162 copying MDTraj/geometry/alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,165 copying MDTraj/geometry/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry 2021-07-09T21:01:01,168 creating build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,169 copying MDTraj/geometry/tests/test_contact.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,171 copying MDTraj/geometry/tests/test_distance.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,173 copying MDTraj/geometry/tests/test_sasa.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,176 copying MDTraj/geometry/tests/test_hbonds.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,178 copying MDTraj/geometry/tests/test_geometry.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,180 copying MDTraj/geometry/tests/test_dihedral.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,183 copying MDTraj/geometry/tests/test_alignment.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,185 copying MDTraj/geometry/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/geometry/tests 2021-07-09T21:01:01,187 creating build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T21:01:01,188 copying MDTraj/core/topology.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T21:01:01,191 copying MDTraj/core/trajectory.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T21:01:01,195 copying MDTraj/core/element.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T21:01:01,198 copying MDTraj/core/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/core 2021-07-09T21:01:01,200 creating build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,201 copying MDTraj/formats/prmtop.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,205 copying MDTraj/formats/mdcrd.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,208 copying MDTraj/formats/openmmxml.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,210 copying MDTraj/formats/arc.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,213 copying MDTraj/formats/lh5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,216 copying MDTraj/formats/netcdf.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,219 copying MDTraj/formats/registry.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,221 copying MDTraj/formats/hdf5.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,225 copying MDTraj/formats/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats 2021-07-09T21:01:01,228 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-09T21:01:01,229 copying MDTraj/formats/pdb/pdbstructure.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-09T21:01:01,232 copying MDTraj/formats/pdb/pdbfile.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-09T21:01:01,235 copying MDTraj/formats/pdb/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb 2021-07-09T21:01:01,238 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-09T21:01:01,239 copying MDTraj/formats/pdb/tests/test_pdb.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-09T21:01:01,241 copying MDTraj/formats/pdb/tests/test_element.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-09T21:01:01,243 copying MDTraj/formats/pdb/tests/__init__.py -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/tests 2021-07-09T21:01:01,251 creating build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,252 copying MDTraj/testing/reference/g_sas_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,264 copying MDTraj/testing/reference/frame0.mdcrdbox -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,285 copying MDTraj/testing/reference/nonconsecutive_resSeq.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,287 copying MDTraj/testing/reference/frame0.xtc.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,293 copying MDTraj/testing/reference/frame0.dcd.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,299 copying MDTraj/testing/reference/atom_distances_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,302 copying MDTraj/testing/reference/traj.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,307 copying MDTraj/testing/reference/Rg_traj_ref.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,309 copying MDTraj/testing/reference/alanine-dipeptide-explicit.prmtop -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,321 copying MDTraj/testing/reference/native2.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,323 copying MDTraj/testing/reference/native2.xml -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,326 copying MDTraj/testing/reference/1bpi.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,330 copying MDTraj/testing/reference/bpti.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,335 copying MDTraj/testing/reference/frame0.binpos.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,341 copying MDTraj/testing/reference/alanine-dipeptide-explicit.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,345 copying MDTraj/testing/reference/4K6Q.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,355 copying MDTraj/testing/reference/frame0.h5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,360 copying MDTraj/testing/reference/cc_ca.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,362 copying MDTraj/testing/reference/1vii_sustiva_water.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,405 copying MDTraj/testing/reference/alanine-dipeptide-explicit.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,411 copying MDTraj/testing/reference/cc_closest.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,413 copying MDTraj/testing/reference/4waters.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,416 copying MDTraj/testing/reference/frame0.trr -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,430 copying MDTraj/testing/reference/atom_pairs.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,432 copying MDTraj/testing/reference/frame0.mdcrd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,446 copying MDTraj/testing/reference/frame0.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,453 copying MDTraj/testing/reference/cc_closest-heavy.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,455 copying MDTraj/testing/reference/mdcrd.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,463 copying MDTraj/testing/reference/legacy_msmbuilder_trj0.lh5 -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,467 copying MDTraj/testing/reference/contacts.dat -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,470 copying MDTraj/testing/reference/4waters.arc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,472 copying MDTraj/testing/reference/alanine.binpos -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,475 copying MDTraj/testing/reference/native.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,477 copying MDTraj/testing/reference/frame0.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,494 copying MDTraj/testing/reference/alanine-dipeptide-implicit.prmtop -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,497 copying MDTraj/testing/reference/multiframe.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,500 copying MDTraj/testing/reference/frame0.dcd -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,508 copying MDTraj/testing/reference/frame0.xtc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,512 copying MDTraj/testing/reference/2EQQ.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,535 copying MDTraj/testing/reference/frame0.nc -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,542 copying MDTraj/testing/reference/GG-tip4pew.pdb -> build/lib.linux-armv7l-3.9/mdtraj/testing/reference 2021-07-09T21:01:01,556 creating build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-09T21:01:01,557 copying MDTraj/formats/pdb/data/pdbNames.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-09T21:01:01,560 copying MDTraj/formats/pdb/data/residues.xml -> build/lib.linux-armv7l-3.9/mdtraj/formats/pdb/data 2021-07-09T21:01:01,575 running build_ext 2021-07-09T21:01:01,641 cythoning MDTraj/formats/xtc/xtc.pyx to MDTraj/formats/xtc/xtc.c 2021-07-09T21:01:02,272 /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-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/MDTraj/formats/xtc/xtc.pyx 2021-07-09T21:01:02,273 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T21:01:04,723 cythoning MDTraj/formats/xtc/trr.pyx to MDTraj/formats/xtc/trr.c 2021-07-09T21:01:04,731 /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-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/MDTraj/formats/xtc/trr.pyx 2021-07-09T21:01:04,732 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T21:01:07,132 cythoning MDTraj/formats/dcd/dcd.pyx to MDTraj/formats/dcd/dcd.c 2021-07-09T21:01:07,144 /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-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/MDTraj/formats/dcd/dcd.pyx 2021-07-09T21:01:07,144 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T21:01:09,480 cythoning MDTraj/formats/binpos/binpos.pyx to MDTraj/formats/binpos/binpos.c 2021-07-09T21:01:09,491 /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-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/MDTraj/formats/binpos/binpos.pyx 2021-07-09T21:01:09,491 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T21:01:11,570 cythoning MDTraj/rmsd/_rmsd.pyx to MDTraj/rmsd/_rmsd.c 2021-07-09T21:01:11,582 /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-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/MDTraj/rmsd/_rmsd.pyx 2021-07-09T21:01:11,582 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-09T21:01:14,743 warning: MDTraj/rmsd/_rmsd.pyx:168:62: Use boundscheck(False) for faster access 2021-07-09T21:01:14,744 warning: MDTraj/rmsd/_rmsd.pyx:168:87: Use boundscheck(False) for faster access 2021-07-09T21:01:14,745 warning: MDTraj/rmsd/_rmsd.pyx:168:103: Use boundscheck(False) for faster access 2021-07-09T21:01:14,745 warning: MDTraj/rmsd/_rmsd.pyx:169:21: Use boundscheck(False) for faster access 2021-07-09T21:01:14,906 building 'mdtraj.formats.xtc' extension 2021-07-09T21:01:14,907 creating build/temp.linux-armv7l-3.9 2021-07-09T21:01:14,908 creating build/temp.linux-armv7l-3.9/MDTraj 2021-07-09T21:01:14,908 creating build/temp.linux-armv7l-3.9/MDTraj/formats 2021-07-09T21:01:14,909 creating build/temp.linux-armv7l-3.9/MDTraj/formats/xtc 2021-07-09T21:01:14,910 creating build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src 2021-07-09T21:01:14,911 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 -IMDTraj/formats/xtc/include/ -IMDTraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src/xdrfile.o 2021-07-09T21:01:15,093 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-09T21:01:15,094 MDTraj/formats/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:15,094 478 | while (size >= num && num_of_bits < 32) 2021-07-09T21:01:15,094 | ^~ 2021-07-09T21:01:15,095 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-09T21:01:15,095 MDTraj/formats/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:15,095 524 | while (bytes[num_of_bytes] >= num) 2021-07-09T21:01:15,095 | ^~ 2021-07-09T21:01:15,097 MDTraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-09T21:01:15,097 MDTraj/formats/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:15,097 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-09T21:01:15,098 | ^~ 2021-07-09T21:01:15,098 MDTraj/formats/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:15,098 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-09T21:01:15,098 | ^ 2021-07-09T21:01:15,099 MDTraj/formats/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:15,099 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-09T21:01:15,099 | ^ 2021-07-09T21:01:15,100 MDTraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-09T21:01:15,100 MDTraj/formats/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:15,100 683 | if (lastbits < num_of_bits) 2021-07-09T21:01:15,101 | ^ 2021-07-09T21:01:15,102 MDTraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-09T21:01:15,103 MDTraj/formats/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:15,103 797 | if(size3>xfp->buf1size) 2021-07-09T21:01:15,103 | ^ 2021-07-09T21:01:15,105 MDTraj/formats/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:15,106 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T21:01:15,112 | ^ 2021-07-09T21:01:15,117 MDTraj/formats/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:15,117 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-09T21:01:15,117 | ^ 2021-07-09T21:01:15,118 MDTraj/formats/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:15,118 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T21:01:15,127 | ^ 2021-07-09T21:01:15,129 MDTraj/formats/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:15,129 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-09T21:01:15,137 | ^ 2021-07-09T21:01:15,143 MDTraj/formats/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:15,143 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-09T21:01:15,143 | ^ 2021-07-09T21:01:15,145 MDTraj/formats/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:15,145 1611 | maxidx = (LASTIDXn_frames == -1L) != 0); 2021-07-09T21:01:18,269 | ^~ 2021-07-09T21:01:18,286 MDTraj/formats/xtc/xtc.c:9252:12: warning: implicit declaration of function ‘read_xtc_nframes’; did you mean ‘read_xtc_natoms’? [-Wimplicit-function-declaration] 2021-07-09T21:01:18,286 9252 | (void)(read_xtc_nframes(__pyx_t_4, (&__pyx_v_self->n_frames))); 2021-07-09T21:01:18,286 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:01:18,286 | read_xtc_natoms 2021-07-09T21:01:22,721 MDTraj/formats/xtc/xtc.c: In function ‘__pyx_pf_6mdtraj_7formats_3xtc_17XTCTrajectoryFile_14_write’: 2021-07-09T21:01:22,722 MDTraj/formats/xtc/xtc.c:526:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T21:01:22,722 526 | #define PyInt_FromLong PyLong_FromLong 2021-07-09T21:01:22,722 | ^~~~~~~~~~~~~~~ 2021-07-09T21:01:22,726 MDTraj/formats/xtc/xtc.c:8013:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T21:01:22,727 8013 | int __pyx_v_status; 2021-07-09T21:01:22,727 | ^~~~~~~~~~~~~~ 2021-07-09T21:01:33,402 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/MDTraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src/xdrfile_xtc.o build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/xtc.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/xtc.cpython-39-arm-linux-gnueabihf.so 2021-07-09T21:01:33,589 building 'mdtraj.formats.trr' extension 2021-07-09T21:01:33,589 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 -IMDTraj/formats/xtc/include/ -IMDTraj/formats/xtc/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/formats/xtc/src/xdrfile.c -o build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src/xdrfile.o 2021-07-09T21:01:33,743 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofint’: 2021-07-09T21:01:33,744 MDTraj/formats/xtc/src/xdrfile.c:478:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:33,744 478 | while (size >= num && num_of_bits < 32) 2021-07-09T21:01:33,744 | ^~ 2021-07-09T21:01:33,744 MDTraj/formats/xtc/src/xdrfile.c: In function ‘sizeofints’: 2021-07-09T21:01:33,744 MDTraj/formats/xtc/src/xdrfile.c:524:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:33,744 524 | while (bytes[num_of_bytes] >= num) 2021-07-09T21:01:33,745 | ^~ 2021-07-09T21:01:33,745 MDTraj/formats/xtc/src/xdrfile.c: In function ‘encodeints’: 2021-07-09T21:01:33,746 MDTraj/formats/xtc/src/xdrfile.c:633:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:33,746 633 | if (num_of_bits >= num_of_bytes * 8) 2021-07-09T21:01:33,746 | ^~ 2021-07-09T21:01:33,746 MDTraj/formats/xtc/src/xdrfile.c:635:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:33,746 635 | for (i = 0; i < num_of_bytes; i++) 2021-07-09T21:01:33,746 | ^ 2021-07-09T21:01:33,747 MDTraj/formats/xtc/src/xdrfile.c:643:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:33,747 643 | for (i = 0; i < num_of_bytes-1; i++) 2021-07-09T21:01:33,747 | ^ 2021-07-09T21:01:33,747 MDTraj/formats/xtc/src/xdrfile.c: In function ‘decodebits’: 2021-07-09T21:01:33,747 MDTraj/formats/xtc/src/xdrfile.c:683:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:33,747 683 | if (lastbits < num_of_bits) 2021-07-09T21:01:33,747 | ^ 2021-07-09T21:01:33,748 MDTraj/formats/xtc/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2021-07-09T21:01:33,749 MDTraj/formats/xtc/src/xdrfile.c:797:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:33,749 797 | if(size3>xfp->buf1size) 2021-07-09T21:01:33,749 | ^ 2021-07-09T21:01:33,750 MDTraj/formats/xtc/src/xdrfile.c:851:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:33,750 851 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T21:01:33,754 | ^ 2021-07-09T21:01:33,758 MDTraj/formats/xtc/src/xdrfile.c:1122:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:33,758 1122 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2021-07-09T21:01:33,759 | ^ 2021-07-09T21:01:33,759 MDTraj/formats/xtc/src/xdrfile.c:1128:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:33,759 1128 | maxidx = (LASTIDXxfp->buf1size) 2021-07-09T21:01:33,765 | ^ 2021-07-09T21:01:33,766 MDTraj/formats/xtc/src/xdrfile.c:1355:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:33,766 1355 | maxidx = (LASTIDXxfp->buf1size) { 2021-07-09T21:01:33,772 | ^ 2021-07-09T21:01:33,778 MDTraj/formats/xtc/src/xdrfile.c:1606:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:01:33,778 1606 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2021-07-09T21:01:33,778 | ^ 2021-07-09T21:01:33,779 MDTraj/formats/xtc/src/xdrfile.c:1611:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:01:33,779 1611 | maxidx = (LASTIDXn_frames == -1L) != 0); 2021-07-09T21:01:37,302 | ^~ 2021-07-09T21:01:41,605 MDTraj/formats/xtc/trr.c: In function ‘__pyx_pf_6mdtraj_7formats_3trr_17TRRTrajectoryFile_14_write’: 2021-07-09T21:01:41,606 MDTraj/formats/xtc/trr.c:526:40: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T21:01:41,606 526 | #define PyInt_FromLong PyLong_FromLong 2021-07-09T21:01:41,606 | ^~~~~~~~~~~~~~~ 2021-07-09T21:01:41,610 MDTraj/formats/xtc/trr.c:7978:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T21:01:41,610 7978 | int __pyx_v_status; 2021-07-09T21:01:41,610 | ^~~~~~~~~~~~~~ 2021-07-09T21:01:52,551 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/MDTraj/formats/xtc/src/xdrfile.o build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/src/xdrfile_trr.o build/temp.linux-armv7l-3.9/MDTraj/formats/xtc/trr.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/trr.cpython-39-arm-linux-gnueabihf.so 2021-07-09T21:01:52,727 building 'mdtraj.formats.dcd' extension 2021-07-09T21:01:52,728 creating build/temp.linux-armv7l-3.9/MDTraj/formats/dcd 2021-07-09T21:01:52,729 creating build/temp.linux-armv7l-3.9/MDTraj/formats/dcd/src 2021-07-09T21:01:52,729 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 -IMDTraj/formats/dcd/include/ -IMDTraj/formats/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/formats/dcd/dcd.c -o build/temp.linux-armv7l-3.9/MDTraj/formats/dcd/dcd.o 2021-07-09T21:01:53,131 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-09T21:01:53,131 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-09T21:01:53,132 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-09T21:01:53,132 from MDTraj/formats/dcd/dcd.c:612: 2021-07-09T21:01:53,132 /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] 2021-07-09T21:01:53,132 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-09T21:01:53,132 | ^~~~~~~ 2021-07-09T21:01:53,265 MDTraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_16__len__’: 2021-07-09T21:01:53,269 MDTraj/formats/dcd/dcd.c:4896:13: warning: implicit declaration of function ‘dcd_nsets’ [-Wimplicit-function-declaration] 2021-07-09T21:01:53,269 4896 | __pyx_r = dcd_nsets(__pyx_v_self->fh); 2021-07-09T21:01:53,269 | ^~~~~~~~~ 2021-07-09T21:01:54,003 In file included from MDTraj/formats/dcd/include/dcdplugin.h:1, 2021-07-09T21:01:54,003 from MDTraj/formats/dcd/dcd.c:621: 2021-07-09T21:01:54,003 At top level: 2021-07-09T21:01:54,003 MDTraj/formats/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-09T21:01:54,003 473 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-09T21:01:54,004 | ^~~~~~~~~~~~~ 2021-07-09T21:01:54,004 MDTraj/formats/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-09T21:01:54,004 469 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-09T21:01:54,004 | ^~~~~~~~~~~~~~ 2021-07-09T21:01:54,004 MDTraj/formats/dcd/include/fastio.h:465:12: warning: ‘fio_write_int32’ defined but not used [-Wunused-function] 2021-07-09T21:01:54,004 465 | static int fio_write_int32(fio_fd fd, int i) { 2021-07-09T21:01:54,004 | ^~~~~~~~~~~~~~~ 2021-07-09T21:01:54,005 MDTraj/formats/dcd/include/fastio.h:456:19: warning: ‘fio_ftell’ defined but not used [-Wunused-function] 2021-07-09T21:01:54,005 456 | static fio_size_t fio_ftell(fio_fd fd) { 2021-07-09T21:01:54,005 | ^~~~~~~~~ 2021-07-09T21:01:54,005 MDTraj/formats/dcd/include/fastio.h:449:19: warning: ‘fio_fseek’ defined but not used [-Wunused-function] 2021-07-09T21:01:54,005 449 | static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) { 2021-07-09T21:01:54,005 | ^~~~~~~~~ 2021-07-09T21:01:54,005 MDTraj/formats/dcd/include/fastio.h:414:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] 2021-07-09T21:01:54,005 414 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { 2021-07-09T21:01:54,006 | ^~~~~~~~~ 2021-07-09T21:01:54,006 MDTraj/formats/dcd/include/fastio.h:393:12: warning: ‘fio_fclose’ defined but not used [-Wunused-function] 2021-07-09T21:01:54,006 393 | static int fio_fclose(fio_fd fd) { 2021-07-09T21:01:54,006 | ^~~~~~~~~~ 2021-07-09T21:01:54,006 MDTraj/formats/dcd/include/fastio.h:365:12: warning: ‘fio_open’ defined but not used [-Wunused-function] 2021-07-09T21:01:54,006 365 | static int fio_open(const char *filename, int mode, fio_fd *fd) { 2021-07-09T21:01:54,006 | ^~~~~~~~ 2021-07-09T21:02:00,498 MDTraj/formats/dcd/dcd.c: In function ‘__pyx_pf_6mdtraj_7formats_3dcd_17DCDTrajectoryFile_18read’: 2021-07-09T21:02:00,499 MDTraj/formats/dcd/dcd.c:526:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T21:02:00,499 526 | #define PyInt_FromLong PyLong_FromLong 2021-07-09T21:02:00,499 | ^~~~~~~~~~~~~~~ 2021-07-09T21:02:00,502 MDTraj/formats/dcd/dcd.c:5019:7: note: ‘__pyx_v_i’ was declared here 2021-07-09T21:02:00,502 5019 | int __pyx_v_i; 2021-07-09T21:02:00,503 | ^~~~~~~~~ 2021-07-09T21:02:03,579 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 -IMDTraj/formats/dcd/include/ -IMDTraj/formats/dcd/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/formats/dcd/src/dcdplugin.c -o build/temp.linux-armv7l-3.9/MDTraj/formats/dcd/src/dcdplugin.o 2021-07-09T21:02:03,819 MDTraj/formats/dcd/src/dcdplugin.c: In function ‘read_dcdheader’: 2021-07-09T21:02:03,819 MDTraj/formats/dcd/src/dcdplugin.c:129:57: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:02:03,819 129 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { 2021-07-09T21:02:03,819 | ^~ 2021-07-09T21:02:03,820 MDTraj/formats/dcd/src/dcdplugin.c:146:54: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:02:03,820 146 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { 2021-07-09T21:02:03,820 | ^~ 2021-07-09T21:02:03,820 MDTraj/formats/dcd/src/dcdplugin.c:164:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:02:03,820 164 | if (input_integer[0] != dcdcordmagic) { 2021-07-09T21:02:03,821 | ^~ 2021-07-09T21:02:03,823 MDTraj/formats/dcd/src/dcdplugin.c:341:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:02:03,824 341 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { 2021-07-09T21:02:03,824 | ^~ 2021-07-09T21:02:03,824 MDTraj/formats/dcd/src/dcdplugin.c:358:45: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-09T21:02:03,824 358 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { 2021-07-09T21:02:03,824 | ^~ 2021-07-09T21:02:03,828 MDTraj/formats/dcd/src/dcdplugin.c: In function ‘read_dcdstep’: 2021-07-09T21:02:03,828 MDTraj/formats/dcd/src/dcdplugin.c:540:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:02:03,828 540 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-09T21:02:03,828 | ^~ 2021-07-09T21:02:03,829 MDTraj/formats/dcd/src/dcdplugin.c:544:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-09T21:02:03,829 544 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; 2021-07-09T21:02:03,829 | ^~ 2021-07-09T21:02:03,853 In file included from MDTraj/formats/dcd/src/dcdplugin.c:55: 2021-07-09T21:02:03,854 At top level: 2021-07-09T21:02:03,854 MDTraj/formats/dcd/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2021-07-09T21:02:03,854 96 | static void swap2_aligned(void *v, long ndata) { 2021-07-09T21:02:03,854 | ^~~~~~~~~~~~~ 2021-07-09T21:02:03,854 MDTraj/formats/dcd/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2021-07-09T21:02:03,855 32 | static void swap2_unaligned(void *v, long ndata) { 2021-07-09T21:02:03,855 | ^~~~~~~~~~~~~~~ 2021-07-09T21:02:03,855 In file included from MDTraj/formats/dcd/src/dcdplugin.c:46: 2021-07-09T21:02:03,855 MDTraj/formats/dcd/include/fastio.h:473:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2021-07-09T21:02:03,855 473 | static int fio_write_str(fio_fd fd, const char *str) { 2021-07-09T21:02:03,855 | ^~~~~~~~~~~~~ 2021-07-09T21:02:03,856 MDTraj/formats/dcd/include/fastio.h:469:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2021-07-09T21:02:03,856 469 | static int fio_read_int32(fio_fd fd, int *i) { 2021-07-09T21:02:03,856 | ^~~~~~~~~~~~~~ 2021-07-09T21:02:05,014 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/MDTraj/formats/dcd/dcd.o build/temp.linux-armv7l-3.9/MDTraj/formats/dcd/src/dcdplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/dcd.cpython-39-arm-linux-gnueabihf.so 2021-07-09T21:02:05,177 building 'mdtraj.formats.binpos' extension 2021-07-09T21:02:05,178 creating build/temp.linux-armv7l-3.9/MDTraj/formats/binpos 2021-07-09T21:02:05,179 creating build/temp.linux-armv7l-3.9/MDTraj/formats/binpos/src 2021-07-09T21:02:05,179 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 -IMDTraj/formats/binpos/include/ -IMDTraj/formats/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/formats/binpos/binpos.c -o build/temp.linux-armv7l-3.9/MDTraj/formats/binpos/binpos.o 2021-07-09T21:02:05,584 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-09T21:02:05,584 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-09T21:02:05,584 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-09T21:02:05,584 from MDTraj/formats/binpos/binpos.c:612: 2021-07-09T21:02:05,584 /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] 2021-07-09T21:02:05,585 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-09T21:02:05,585 | ^~~~~~~ 2021-07-09T21:02:11,772 MDTraj/formats/binpos/binpos.c: In function ‘__pyx_pw_6mdtraj_7formats_6binpos_20BINPOSTrajectoryFile_7_read’: 2021-07-09T21:02:11,774 MDTraj/formats/binpos/binpos.c:4842:6: warning: ‘__pyx_v_status’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T21:02:11,775 4842 | if (__pyx_t_2) { 2021-07-09T21:02:11,775 | ^ 2021-07-09T21:02:11,777 MDTraj/formats/binpos/binpos.c:4322:7: note: ‘__pyx_v_status’ was declared here 2021-07-09T21:02:11,777 4322 | int __pyx_v_status; 2021-07-09T21:02:11,777 | ^~~~~~~~~~~~~~ 2021-07-09T21:02:11,777 MDTraj/formats/binpos/binpos.c:526:40: warning: ‘__pyx_v_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-09T21:02:11,778 526 | #define PyInt_FromLong PyLong_FromLong 2021-07-09T21:02:11,778 | ^~~~~~~~~~~~~~~ 2021-07-09T21:02:11,780 MDTraj/formats/binpos/binpos.c:4319:7: note: ‘__pyx_v_i’ was declared here 2021-07-09T21:02:11,780 4319 | int __pyx_v_i; 2021-07-09T21:02:11,780 | ^~~~~~~~~ 2021-07-09T21:02:14,324 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 -IMDTraj/formats/binpos/include/ -IMDTraj/formats/binpos/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/formats/binpos/src/binposplugin.c -o build/temp.linux-armv7l-3.9/MDTraj/formats/binpos/src/binposplugin.o 2021-07-09T21:02:14,454 MDTraj/formats/binpos/src/binposplugin.c: In function ‘seek_timestep’: 2021-07-09T21:02:14,455 MDTraj/formats/binpos/src/binposplugin.c:105:9: warning: unused variable ‘i’ [-Wunused-variable] 2021-07-09T21:02:14,455 105 | int i, numatoms; 2021-07-09T21:02:14,455 | ^ 2021-07-09T21:02:14,455 MDTraj/formats/binpos/src/binposplugin.c: In function ‘tell_timestep’: 2021-07-09T21:02:14,456 MDTraj/formats/binpos/src/binposplugin.c:128:9: warning: unused variable ‘i’ [-Wunused-variable] 2021-07-09T21:02:14,456 128 | int i, numatoms, frame; 2021-07-09T21:02:14,456 | ^ 2021-07-09T21:02:14,683 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/MDTraj/formats/binpos/binpos.o build/temp.linux-armv7l-3.9/MDTraj/formats/binpos/src/binposplugin.o -o build/lib.linux-armv7l-3.9/mdtraj/formats/binpos.cpython-39-arm-linux-gnueabihf.so 2021-07-09T21:02:14,836 building 'mdtraj._rmsd' extension 2021-07-09T21:02:14,836 creating build/temp.linux-armv7l-3.9/MDTraj/rmsd 2021-07-09T21:02:14,837 creating build/temp.linux-armv7l-3.9/MDTraj/rmsd/src 2021-07-09T21:02:14,843 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 -IMDTraj/rmsd/include -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c MDTraj/rmsd/_rmsd.c -o build/temp.linux-armv7l-3.9/MDTraj/rmsd/_rmsd.o -msse2 -O3 -funroll-loops -fopenmp 2021-07-09T21:02:14,859 arm-linux-gnueabihf-gcc: error: unrecognized command-line option ‘-msse2’ 2021-07-09T21:02:14,862 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T21:02:15,123 Building wheel for mdtraj (setup.py): finished with status 'error' 2021-07-09T21:02:15,124 ERROR: Failed building wheel for mdtraj 2021-07-09T21:02:15,125 Running setup.py clean for mdtraj 2021-07-09T21:02:15,125 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-xu7gb3jz/mdtraj_74a30d8837c745bbb6f8ac07ff4e1c42/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'"'"'))' clean --all 2021-07-09T21:02:16,647 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2021-07-09T21:02:16,850 running clean 2021-07-09T21:02:16,852 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T21:02:16,865 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T21:02:16,930 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T21:02:16,931 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T21:02:16,931 removing 'build' 2021-07-09T21:02:17,031 Failed to build mdtraj 2021-07-09T21:02:17,032 ERROR: Failed to build one or more wheels 2021-07-09T21:02:17,032 Exception information: 2021-07-09T21:02:17,032 Traceback (most recent call last): 2021-07-09T21:02:17,032 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T21:02:17,032 status = self.run(options, args) 2021-07-09T21:02:17,032 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T21:02:17,032 return func(self, options, args) 2021-07-09T21:02:17,032 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T21:02:17,032 raise CommandError( 2021-07-09T21:02:17,032 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T21:02:17,036 Removed build tracker: '/tmp/pip-req-tracker-q6uo47dl'